Cool to see the games being worked on! I don't think most of these are related to your goals but they're the things I'd most like to see changed for MML1 (haven't played 2 yet) after beating it a few months back so it seems like the best place to post them:
-Mostly linear structure (you can sometimes choose between two dungeons but you're guided towards the "right" one and picking the other one is kind of redundant since the game doesn't let you explore it fully at that point, you'll gain new abilites over the course of the game which let you explore previous areas fully)
-Some enemies won't even react if shot from far enough away
-Your mines don't hurt you if you stand right next to an enemy and drop them (this does lots of damage quickly)
-Some control issues (very short invincibility time means you'll get hit several times in a row by some attacks and can get pinned down by multiple enemies in some situations, can't change targets while auto-aiming, minor delay after jumping and side dodging, some delay before using certain special weapons (and not being able to move while shooting) make them near useless against some bosses, have to touch a tile for the auto-mapper to fill it in which creates situations where it looks like there might be a path where you haven't explored 100% of a room, can't look around/aim while moving, can't move backwards while shooting)
-Can shoot faster manually by moving forward slightly between shots - Maybe it should be easier to fire that fast without a weird trick, so it's more like the 2D games?
-The (default) vacuum arm special weapon should be a default passive ability imo, as it makes for a better gameplay flow
-Some special weapons aren't very good (drill - good for destroying certain walls at least, grenade, blade, shield - can't move nor shoot at the same time, machine? - avoid upgrading its special (spread))