Carson was the first character we saw seated in a Control Chair back in "Rising" and he (or at least his clone) gets to be the last one seated for the finale, so to speak.
Additionally like in "Rising," Carson is firing drones at a ship Sheppard is on. This time instead of accidentally in a panic, he's deliberately firing on a hive ship.
Atlantis left Earth and the Milky Way Galaxy in the Pilot and now returns home for the Finale.
The Bus Came Back: Major Paul Davis returns to Stargate for the first time since his cameo in Stargate: Continuum and his first TV appearance since SG-1 Season Eight ("Moebius, Pt. 1"). This is not only his first and only appearance on Atlantis, but also the final appearance of Davis in the franchise (as the character would not appear on Universe before its cancellation). This ends a run for Cunningham that had begun a decade earlier with the SG-1 Season Two episode "A Matter of Time".
Call-Back: The Super Hive gets nuked in orbit much in the same way Ra's ship was destroyed in the original Stargate film.
Sheppard's team uses a stargate on the hive to escape its destruction. SG-1 did this on at least three occasions: "The Serpent's Lair", "Nemesis", and "Off the Grid".
The Wraith once again dial a targeted planet's Stargate to prevent their prey from escaping the Culling.
Like in "Lost City Part 2", said dial-in prevents politicians from escaping to the Alpha Site.
Crippling Overspecialization: This is more or less the reason why the Asgard plasma beam weapons weren't able to significantly damage the super hive. They were designed specifically to take down *shielded* targets, by concentrating a huge amount of energy on a tiny part of the shield, allowing it to break through just about anything (even Ori shields). Unfortunately, Wraith hives don't use shields, they just have really thick hulls (the super ZPM powered hive even moreso), so all the beams could do was poke tiny holes in the ship, which could very quickly be regenerated due to it being a Living Ship with virtually unlimited power due to an unknown number of ZPM's.
Deus ex Nukina: Continuing the grand Stargate tradition. This is also the franchise's final Ex Nukina.
Disney Death: Ronon on the Hive. Luckily, he's brought back by one of the Wraith and rescued.
Exact Words: Woolsey and the others finally realize Todd did this back during "Spoils of War". He said he acquired several ZPMs when Asruas blew up. Todd being Todd, he never actually stated how many ZPM's constituted 'several' (or whether they were all used at the Cloning Facility).
Foreshadowing: Caldwell mentions the Odyssey is unavailable to help attack the Super-Hive due to some kind of top-secret mission. According to Joseph Mallozzi, this mission was Icarus Base and thus was quietly setting up Stargate Universe.
Grand Finale: Though it wasn't intended as such originally.
Hoist by Their Own Petard: The Wraith's usual tactic of dialing the Stargate of a world being Culled to prevent their prey from escaping. It cuts off the SGC Gate (see Technology Marches On), but it also unwittingly gives the Expedition a backdoor into the Super-Hive.
Meaningful Rename: Carter reveals that the Phoenix is being renamed the General Hammond, in honor of their fallen leader.
New Powers as the Plot Demands: The Wormhole Drive. The cancellation of the series meant that it unfortunately gave no time for it to be set up beforehand, making it come across as something of an Ass Pull from an audience perspective. It would have been further explained in the subsequent movie, but unfortunately that was cancelled too.
Nice Job Breaking It, Hero: The Ancient Control Chair is revealed to have been moved to Area 51, due to being technically in violation of the treaty on the non-proliferation of weapons in Antarctica. As a result, it ended up being exactly where the Wraith information from the other reality said it would be, allowing them to easily wipe out Earth's last line of defense. Oops. Although Atlantis' own drones were revealed to be virtually useless against the hive, there's no reason to assume the drones on earth would have been any more effective.
Screw This, I'm Outta Here: The I.O.A. are mentioned as being the first in line to evacuate to the Alpha Site, leading Major Davis to applauds their bravery. Unfortunately for them, they didn't count on the Wraith Hive having a Stargate onboard to block their dial-out.
Simultaneous Arcs: With "Vegas". The series finale syncs up with the ending of the previous episode (when the Wraith signal transmits) during the first failed attack on the Super Hive.
An especially egregious example. Apart from Carter (and O'Neill issuing orders off-screen from Washington), none of SG-1 appear to lend a hand against the impending invasion. This for better and for worse can be justified between budget concerns, actor availability, and wanting to keep the focus on the Atlantis crew rather than their sister team (as this was the spinoff's Grand Finale and 100th episode).
Zigzagged with the Odyssey. The first post-Daedelus BC-304 is likewise unavailable, but this again was meant to be setup for Stargate Universe.
Technology Marches On: An in-universe variation. It's revealed that because the Pegasus Gates were manufactured after the Ancients had left the Milky Way, their system OS automatically supersedes any older Gate models in the vicinity like the Milky Way Network. The Wraith use this to cut off the SGC's Gate during the culling of Earth, but it also allows the Expedition to send a team in behind enemy lines on their end.
Villain Has a Point: When Woolsey demands to know how many Zero Point Modules Todd actually salvaged from Asuras, the Wraith dismisses it as "unnecessary details". When Woolsey presses again, Todds points out that even if he gave the Expedition that number, they'd have no way of verifying it — and that's assuming they even believe him in the first place, which Todd knows they won't. So what's the point? Woosley begrudgingly realizes Todd's right and abandons this line of inquiry for the moment.
Technology Marches On), but it also unwittingly gives the Expedition a backdoor into the Super-Hive.
Ass Pull from an audience perspective. It would have been further explained in the subsequent movie, but unfortunately that was cancelled too.