Combination Attack: Advance is not the first appearance of the Final Dynamic Special and the Combination Attack (that would be 64), it is the first handheld with this function, and would set up for every other handheld having them.
Expy: With the exception of the Gespenst, all original mecha in Advance are cut-and-paste copies of the original machines from 64, which led to Wild Mass Guessing by fans the 64 and Advance stories are interconnected, until Word of GodJossed this.
What makes this guessing so spot-on is how the Advance back-story is closely identical to the 64 plot: the Shadow-Mirror and the Original Generation villains from 64 have the same motivations, along with the 64 protagonists winding up as a sort-of "heroic" Shadow-Mirror equivalent. Additionally, both games feature a reference to the Gespenst MK III, better known by its codename "Alt Eisen" from Super Robot Wars Compact 2. Considering how current SRW series producer Takenobu Terada treats the fanbase...
Heroic Sacrifice: Richter and Raiza, though not by throwing themselves into the sun like how Richter did it in the original series, but blowing themselves up in a nuclear level explosion, wiping out half of the army of the Vegan Alliance.
Subverted in the case for the chosen protagonist, who fails to kill the Big Bad by self-detonating his/her machine.
Made of Iron, No One Could Survive That: This explains why Axel/Lamia survived after self-detonating their machines to protect the heroes. If this doesn't impress you, how about surviving after being punched by both Domon Kasshu and Kazuya Ryuuzaki? For Lamia, she gets hit RIGHT AT THE VITALS and shrugs them off just fine, though relatively justified since she's an android, but for Axel, he manages to stay on his feet, clutching his stomach. It's later revealed Domon and Kazuya BARELY missed his vitals; Axel vaguely dodged it by reflex.
Mid-Season Upgrade: One of the few instances in SRW where it's averted - Axel and Lamia's starting machine gets upgraded in no way, shape, or form. The closest you get is unlocking the mecha's final attack when they hit level 20, but Level Grinding can get you the attack quite quickly.
Additionally, what added the spike in overall difficulty is "Successive Target Adjustment" (more commonly known as "evasion decay"), a system which reduces a unit's chance of evading an attack on the same turn each time it successfully dodge.
Exclusively in A Portable, mixed alongside Actor Allusion, there's a chance Axel will say "LISTEN TO MY SCREAM!! - now's not the time to be saying that!" Nobutoshi Canna voices Axel and Basara Nekki of Macross 7.