Funnily enough, i have some ideas for the mod similar to those, but regarding the armors:
-Considering that Gaia has a giga attack, naturally the Second Armor would also have it in some way or form, like maybe beating certain enemies to charge it to then release it. In a similar form to TF2 (with soldier's banners) and Shadow The Hedgehog, with a bit of MMZXA showing the radius the giga attack will cover. Or alternatively it could just recharge itself jus like Gaia, but in a much slower pace to avoid constant spamming.
-Despite the fact that Fourth and Ultimate are not present, i have a pretty basic idea of how the hover would work: It'll more or less like the games, except you can go pretty much everywhere; Once you jump, press A again to hover, A again to go up, Z to go down, and X, Z (dash) or Y (ground pound) to cancel hover. Additionally it could have a dedicated meter and/or a sound/visual cues to notify the durability of the hover. This could be also apply to Axl if wanted to.
-Speaking of the same armors, perhaps the four charged shots are reserved for Fourth, and the Plasma shot for Ultimate. Or combine both since both armors are essentially the same, in the following order (taken from MMX innocent impulse): Standard Shot, Semi-charged Shot, Normal Charged shot, Four charged shots, Plasma charged shot.
I would yap about the other armors of the series and other minor ideas but that's it for now, don't really want to write a lot of text.