Anti-Climax Boss: The Angels in Alpha are built up to be incredibly dangerous, and each one appears in a unique scenario. Unfortunately, as far as scenario bosses goes, they're incredibly easy, even if players are going for Skill Points or other secrets. Either the Angels are this trope or they're purely inserted into the game for nothing else but show (the fifth Angel Ramiel, for example, doesn't need to be interacted with in a meaningful manner during its appearance).
Particular points for this goes to the fourteeth Angel Zeruel: in the show, this creature's an unstoppable death machine. In the game, thanks to the "Demoralize" Spirit Command from Rei Ayanami, Zeruel is relatively easy to take him down without the Evangelion Unit-01 becoming The Berserker. Hell, Zeruel hits so soft it can actually be a challenge to get Shinji Ikarikilled for the mandatory event to play out in the scenarionote Resulting in the "S2 Engine" upgrade for the Unit-01 unless, instead of lowering Zeruel's Will, players intentionally hit it with weak attacks just to build up its Will pool.
The Final Bosses in Alpha 2 and Alpha 3. For the former, after coming out of the hellish Mobile Suit Gundam: Char's Counterattack scenarios (pitting the player against pretty much every named Gundam antagonist still alive), the finale is considerably easier with no rush for a Skill Point, enabling players to take their sweet time wearing down the boss' immense defenses. Alpha 3, on the other hand, can be easily exploited by positioning allied units at a certain point on the map where the boss will appear, then dog-piling on it, enabling players to end the scenario in one turn, in spite of the boss' high Hit Points.
Critical Research Failure: During the Archangel's descent to Earth in Alpha 3, Murrue mentions that the ZAFT pilots cannot target the refugee ship they released, citing the Antarctic Treaty. Even ignoring the fact that the Antarctic Treaty became defunct when the One Year War ended in the original show, the treaty was signed between the Earth Federation and Zeon, and ZAFT is not bound by it at all.
Demonic Spiders: Ghost X-9s have INSANELY high evasion rates, making them nigh untouchable to even the most accurate and agile Real Robots; it's nearly impossible to hit them without using the "Strike" Spirit Commandnote Increase accuracy to 100% for one turn. Thankfully, they don't show up much.
The Aura Battler Mooks in Alpha; all come with an "Aura Barrier" that can absorb a fair amount of beam-type damage. This isn't so much of a concern early in the game, but when stronger Aura Battler units appear late-game, they come bundled with a fair rating of armor. As the absorption is calculated after damage reduction from armor, this means hurting even grunts, never mind Aura Battler boss units, with beam weaponry can become annoying. Unfortunately, this leads to another problem: most Aura Battler Mooks are "S" size. The best units for clearing them out would be Mobile Suits, but they can't damage them reliably. This forces players to either use Super Robots, while others must invest Spirit Points into Spirit Commands like "Strike", lean real hard on the Macross and Aura Battler Dunbine units, or just pray the Level Scaling in damage is faster for allied units than Mooks.
Good Bad Bugs: "Phase-Shift Armor" ability for the Mobile Suit Gundam SEED units in Alpha 3. It reduces damage from a lot more things than it says it does, including energy beams that aren't close enough to what would be a considered a "beam" in Gundam terminology. For example, "Breast Fire" is not considered a beam attack in the game. This problem was rectified for later SRW games, where energy based attacks from other shows ignore PS Armor.
The Sega Dreamcast version of Alpha has an odd bug where unit "Limit" is disregarded - it doesn't actually limit anything. The only reason to upgrade it is to get the "Full Upgrade Bonus".
There's a funny little infinite cash bug in Scenario 58 of Alpha (PlayStation version only), where if the Spirit Command "Provoke" is used on Tashiro, every move allied units make will rake in roughly 50,000 credits until someone attacks a target. By the end of a player turn, expect a metric asston of credits.
Ho Yay: Averted for the Alpha originals, much like it was in Super Robot Wars 4. When choosing the protagonist's (romantic) partner, it must be of the opposite sex, without exception. The game has no support for same-sex pairings, not even non-explicitly-romantic ones.
Player Punch: You want Zeta Gundam's exceptionally good final attack in Alpha Gaiden? Make sure you kill the Brainwashed and Crazy Rosamia, who can be saved, otherwise.
The Scrappy: Katz Kobayashi remains as annoying as he is in Zeta Gundam. He even expresses racism similar to the Blue Cosmos in Alpha 3 (though Kamille quickly corrects him). No surprises that he keeps getting labeled as "expendable" in various manga adapatations of Alpha.
That One Level: The Information High sequence in Alpha 3. Due to the singing by Sharon Apple, players cannot use Spirit Commands until a certain point in the scenario. The knife-twister? At the very beginning, only two allied units are on the field: Isamu Alva Dyson's YF-19 and Guld Goa Bowman's YF-21. Worse, Ghost-X9s are the enemy, so unless money has been poured onto the mobility stats of the YF-19 and YF-21, it's considered luck if their accuracy gets above 30%. Acquiring the Skill Point is also a Luck-Based Mission.
The Turn X scenario in Alpha Gaiden. This is around the time where the game hates players for getting this far: not only is the Turn X, at this point, the strongest enemy in the game with high strength, accuracy and maneuverability, but Spirit Commands are needed for most attacks to both hit it and not die from the Gym's counterattacks. Unfortunately, the Turn X comes with a high percentage of Regenerating Health, flanked by two powerful Mooks with "Support Attack"/"Support Defend" and Gym will cast "Guts"note Restore HP to max once half his HP is gone (though the latter's due to a triggered event). The field itself has a large group of enemies standing between allied units and the Turn X, on top of a turn limit of 10-18 turns (depending on difficulty).
The best part? This scenario is the time where the Difficulty Spike becomes apparent. Fortunately, in the last few scenarios after that, Breather Levels kick in, only for the game to be rendered cruel again, particularly scenarios 42, 43 and 45 (ESPECIALLY 43). However, despite its That One Level status, Turn X is merely a Wake-Up Call Boss.
That One Boss: R-Gun Rivale in Original Generation. In spite of the machine having more health than the game displays, the scenario it appears in grants it powerful, low-cost weaponry, Regenerating Health and a protective Warp Field that halves all damage. Worse, in order to achieve the Battle Mastery for the scenario, you must lower its HP to zero in seven turns. What most players find so difficult about the Rivale isn't so much that it's That One Boss, but there was never any build-up to it appearing at all.
Americans Are "Meh" About Kusuha: The majority of the international fanbase only know Kusuha via the Original Generation games via the Game Boy Advance, where not only is she unpopular due to her constant Damsel in Distress issues, but is statistically a below-average pilot. A fair cop in that context - Kusuha basically gets into trouble like the "partner" character from Alpha, rather than the protagonist, thus her skill set and stats aren't what they were in Alpha. This also frustrates those more familiar with the franchise, because they know she's much more capable in her own games (or even in the Second Original Generation).
Alternate Character Interpretation: In the Divine Wars TV series for Original Generation, Leona participates in the final battle between the Earth Federation Army and United Colony Corps; in the games, she's ordered not to by her commander Julia Heinkel.
Additionally, in the manga Record of ATX, Leona and few surviving members of the Troye Unit make the decision to join up with the Hagane and Hiryu Custom battleships right before the Divine Crusaders invades Geneva, Switzerland (Federation government headquarters). While Leona does the same thing in Divine Wars, only after the DC has been defeated in Geneva does she wind up aligning with the heroes (in this case, her cousin Elzam had to persuade her).
Alternate Character Interpretation: The InspectorAnimated Adaptation took steps to rewrite her portrayal in Original Generation 2, including her rivalry with Ibis. After escaping from the Tesla-Leicht Institute, Sleigh sticks around to not only protect the Tesla-Leicht transports from the Inspectors (as Ibis' Calion is shot down in the previous episode and Kusuha decides to not deploy in her Grungust Type-3), but to later witness Ibis handle the Astelion with considerable talent. Sleigh realizes Ibis is more committed to Project Terrestrial Dream than she is and chooses to join up with Ratsel on the Kurogane battleship instead of fleeing to the Neo Divine Crusaders. When Sanger and Ratsel assault Tesla-Leicht to liberate it from the Inspectors, Sleigh assists them; however, she opts to retreat back to the Kurogane instead of joining up with Ibis and Tsugumi. Most players agree The Inspectors handled this much better than Original Generation 2.
Foe Yay, Les Yay: With Ibis; a source of frustration for her as her odds at landing a guy aren't looking good when she's surrounded by plenty of girls.
OT3: The fandom likes to pair Arado, Seolla and Cobray together as a...er, "happy trio".
OT3: Some fans present Seolla as someone who doesn't mind... "switching" between her long-time partner Arado and their friend Cobray.
Moe: No one can say they don't want to hug her when she smiles.
Uncanny Valley: In her persona as Nashim Gan Eden, when she opens her eyes, they become unusually big.
Counterpart Comparison: With Bullet; lampshaded in Alpha 3, wherein upon completing all routes in the game, a special scenario featuring the Original Generation has Minaki Tomine and Kusuha notice the vocal and facial similarities between the two, wondering if they're related.
Nightmare Fuel: Keisar Ephes..."End of the Galaxy" final attack: AAAAAHHH!!!
The Ideon Ending plays up the Be Invoked movie, but instead of Ascend to a Higher Plane of Existence, Keisar Ephes swoops in, corrupts Messiah and takes over every soul, condemning them all to his personal Hell as his playthings. No Mind Screw here: what's clear is that you're going to Hell. YIKES.