Despite being airworthy and its nation under American attack, why was that one enemy F-14 not airborne searching for Dagger Squadron, but still stuck in its hanger? Most likely because its ejection seats were faulty and still had not been maintained or replaced. Therefore, no enemy pilots in their right mind wanted to fly it. In their desperation to return to the carrier, Maverick and Rooster learn that the hard way.
There's also the fact that the airbase had just been bombed by the US Navy's Tomahawk missiles attack, taking the runway out of commission. The enemy couldn't get the F-14 off the ground even if they wanted to because to them, it's impossible, which also explains why the F-14 hangar is conveniently empty and unguarded when Maverick and Rooster snuck into it. Maverick being Maverick, he manages to get the plane off the ground anyway due to his exceptional skills, though he lost the front landing gear in the process.
It's actually simpler than that. Mav and Rooster simply didn't arm the Ejection Seats. Maverick went from a Tomcat to an F-5 or A-4 at Top Gun, and likely to a Hornet after that for the remainder of his career. Rooster on the other hand had never been in a Tomcat operationally, so he likely never knew where the ejection seat arming switch even was. Since both had been flying the Hornet, they likely build the muscle memory to flip the arming lever by their right knee. Now, yes, if they bothered to check, it's entirely possible they would've realized it sooner... however they were still in an enemy base and needed to get out of there.
Also, the base had been hit by the missile strike very recently. It's entirely possible none of the Tomcat pilots on the ground were in any condition to fly anyways, whether dead, injured, or trying to make their way across the bombed base.
Maverick's explanation of "GPS jamming" is meaningless as the F-35 can lase its own targets, but there are other reasons the F-35 might not be ideal:
Plausible deniability, thought that is super implausible with a carrier right off the coast.
The F-35s software only allowing maneuvers up to 9G, while the pop-up attack subjects the plane to 10G.
The risk of losing an F-35 to a foreign adversary is too high.
Lasing a tiny target while trying not to black out, while trying to not crash into a mountain, may be too much for one pilot, necessitating a WSO; there are no two-seater F-35 variants currently in service.
Those who know the Tomcat, either because they've flown it, read the NATOPS, or flew it in true sims, will know that the F-14 carries 676 rounds of 20mm Ammo for its M61 Vulcan Cannon. However, when the fight starts, it appears that this Tomcat has less than 200 rounds of ammo loaded. On hearing the gun fire, it's too slow to be a Vulcannote which can spit out rounds so fast it you can't make out individual shots. It's likely that the Rogue Nation may have modified their Tomcats to use a different gun in order to maintain easier logistics, possibly a single-barrel autocannon similar to that used in Russian fighters.
Out of universe, only having 200 rounds and firing so slow allows most viewers to understand the action - the average viewer would mistake the tracers for actual bullets. In universe, Iran tried various upgrades and workarounds to keep the F-14 and F-4 in the air as spare parts became scarce. The Rogue Nation may have down-rated the M61 and only load 200 rounds on their Tomcats to extend its life.
The F-14’s cannon can actually toggle between low and high rates of fire in real life. It’s entirely possible that this Tomcat was set to the low rate of fire and Maverick didn’t switch to the high setting to help conserve ammo. Either that or he simply forgot about that function after spending almost 2 decades out of the F-14’s cockpit.
Despite the technological difference, the dogfight between the Tomcat and the Felon is actually much more even than it seems. The Felon’s main advantage, stealth, is completely lost when in dogfighting range. Its other advantage, super-maneuverability, works as a last-ditch attempt to dodge a missile or get behind an enemy plane, but it leaves the Felon with almost no speed. If the pilot tried something like this again, Maverick wouldn’t have been as surprised and he could have easily gunned down the Felon while it was still slow. Mav and Rooster may have been right about skill trumping tech, but even then, the Felon’s tech wouldn’t have helped it much to begin with.
In both movies Maverick has an... "eventful" first day in the program, both times violating the hard deck and incurring the wrath of his superior officer. But the two occasions also show the difference between Maverick the cocky youth and his older, more mature self. In the first movie Maverick was just showing off and Viper coolly reproaches him, with Maverick accepting the deserved reprimand. In the sequel Maverick is trying to deliver a needed ego-deflating lesson to the younger Top Gun graduates, and calmly argues his case to the loudly angry Cyclone.
Maverick training his students to not only complete their mission but also come home isn't just sentimental, it's also practical: He's been given the best pilots the Navy has to offer and if he loses them, the Navy will have to train another batch to reach that level, which is not going to be easy or cheap.
The Hawkeye crew spotted the two Felons flying their patrol early in the mission, but the third Felon was a total surprise to the flyers and the audience alike. Two reasons for this: The Felons are stealthy, similar to the American F-35s, making them harder to detect on radar, and more importantly, its late arrival (returning from further out in response to the airfield attack, most likely) probably means the Hawkeye crew didn't have a chance to warn Dagger Squadron before Maverick and Rooster went down, and Rooster wasn't able to get the radio working before the end of the fight, so they would have missed any warning calls. In fact, the distress beacon he used to signal their identity before approaching the coast likely drew the attention of the third Felon.
Maverick is a highly decorated aviator, and even Admiral Caine notes that with his skills and experience, even he should be an Admiral by now if he'd only apply himself and practice a little self-discipline. Throughout the film he expresses an all-encompassing desire to find a way to accomplish the mission and bring the pilots back home safely. There's a very strong implication that Maverick has been acting out his whole career to avoid a situation where he would be responsible for the lives of dozens of aviators while being trapped behind a desk like Cyclone, unable to apply his own skills to help them. The last vestiges of the irresponsible hothead from 1986, or the lifelong results of the traumatic loss of Goose, something that nobody except Maverick holds him responsible for.
On that note, Iceman also felt responsible for Goose's death, so that also likely influences his decision to look after Mav and help him look over Rooster.
How does Hangman get the drop on the third Felon? We see earlier in the film that the Super Hornets have trouble spotting bogies that are behind them. Assuming the Felon has a similar blindspot, Hangman might have shut off his own radar and let the Hawkeye crew vector him in behind the Felon while the pilot was distracted trying to run down Maverick and Rooster. Once he was in position, he could loose a heat-seeking Sidewinder at the Felon without giving him the warning of a radar lock.
Beyond that, the closer to the battle group the dogfight got, the more susceptible the Felon would be to any ECM the carrier group might try to employ to mask Hangman's approach, both from the surface ships and any planes in the air. Additionally, the F/A-18E is a "4.5th Generation" fighter, which incorporates "low-observable" design features that make it more difficult to detect on radar when compared to something like a Tomcat.
As for what that third Felon was doing out at sea, it was probably trying to intercept the retreating Dagger Squad. When he didn't catch them in time, he turned his attention to Maverick and Rooster, which further gave Hangman the chance to angle in on him.
Although the mission was a success, the fact that the enemy's nuclear research facility was entirely underground means that the true extent of the damage done by the successful US Navy air raid is unknown. Thus, it is possible for the rogue state to restart and recover what progress they made before it was destroyed by Dagger Squadron, albeit in many years and with great costs. Also, in the time since Dagger Squadron's strike, the enemy would have studied not only why it was successful in the first place, but also what new defenses should be created and what new tactics should be adopted in order to prevent a repeat of Maverick's strategy being used with the same extent of success. Therefore, Maverick and Dagger Squadron's hard work and courage likely would only have delayed the rogue country's acquirement of nuclear weapons.
The aftermath of the site when Rooster dropped the bomb into the facility showed the entire ground erupting like a sudden earthquake, suggesting that the entire underground facility was completely destroyed by the chain reaction. If the enemy nation doesn't have any other nuclear sites someplace else, it's probably safe to say that the nation's capacity to build nuclear weapons is effectively neutralized for a long time.
The film's ending becomes much less joyful and satisfying when one look beyond Maverick's retirement, his rekindled relationship with Penny, and his reconciliation with Rooster. The United States has just attacked a sovereign country whose only "provocation" against the world's foremost superpower was that it was running a nuclear weapons program and receiving military aid from Russia; the 2K12 Kub anti-air missiles, the Mi-28 attack helicopter, and the Su-57 fighter jets are Russian in origin. The American attack has left hundreds to thousands of said country's military personnel and civilian staff dead and even more wounded, which is going to allow said country's government to rally their populace into a furor of anti-American rage. Worse, two American jets were shot down and despite their pilots having escaped, their wreckage and ejection seats were captured. This makes it impossible for the US to plausibly deny that it was the US Navy behind the attacks. Maverick days of flying and fighting are now over, but Rooster and the rest of Dagger Squadron's have not. While Maverick settles down to retire, his trainees will be sent back abroad to fend off the enemy country's attempts to retaliate for the American bombing of their homeland, and it's very likely that members of Dagger Squadron (perhaps even Rooster) will be killed, wounded, or captured in the subsequent conflicts against the "rogue nation".
Sure, it can be denied; it's not just the US that operates the Super Hornet. So unless they were dumb enough to go in piloting jets with their names stenciled on the sides...
Counterpoint, this is the exact same scenario of a raid as Operation Opera, which set back Iraq's nuclear program, and notably did not lead to open war between Iraq and Israel.
As long as it doesn't escalate into a large-scale conflict in which the rogue nation manages to rally allies to its cause, which most likely includes Russia due to the equipment they had in their arsenal, it's unlikely that the rogue nation could do anything on its own against NATO. They had just lost their capacity to create nuclear weapons and a substantial part of its air force is destroyed (at least half a dozen fifth-generation fighters, which may or may not be all that they have: those things don't come cheap), which would discourage any open conflict against various a world superpower and its NATO allies.
Also, this rogue nation is developing a nuclear weapons program that is in direct violation of a NATO treaty. I don't care who you are or where you're from; that is the definition of a provocation of war, and the United States was well within its rights to take defensive action.
Further, the fact that the younger generation of pilots will continue to bear the burden long after Maverick lays down his sword is part and parcel with the film's central thesis: It's time for Maverick to let go and accept that there are some things beyond his control. He has to accept Iceman's death, Rooster's decision to endanger his own life as a naval aviator, and the fact that he can't keep flying and fighting forever.
Penny Benjamin. If we assume Penny is roughly the same age as the actress playing her (Jennifer Connelly), that means Mav was messing around with a girl who was, at the oldest, 16-years-old and possibly younger than that depending on when it was the two of them "went ballistic." Top that off with her being an admiral's daughter, and it's a wonder he didn't get into A LOT more trouble than he did back in the day.
Why do we have to assume that? It's not at all unreasonable to think that Connelly is playing a character three to five years older than her real age — actresses do it all the time, especially when they're as agelessly beautiful as someone like Jennifer Connelly. Penny could very easily have been college-aged during her first relationship with Mav, which would make her about nineteen or twenty to his mid-twenties — a bit eyebrow-raising today, sure, but hardly condemnable.
, which set back Iraq's nuclear program, and notably did not lead to open war between Iraq and Israel.