The idea I have is that say you defeat: BOSS A Now it is a maybe early or semi-early boss that you defeat with some challenge to it, to compare it with terraria it'd be something like the eye of cthulhu and after you beat this thing. If its intelligent enough for like power armour and survived or if its a monster like something similar to cell from Dragon Ball then it regenrates when you thought it dead and it is no stronger. This can lead to also intresting story background and dialogue with the bosses such as them feeling happier at you dying or such because you killed them etc. and tougher challenge without having to do much work. This Now leads to this: Boss A Has move Acid Spit Boss A V.2 has move Super Acid Spit This and such would lead to tougher challenge but remaining familiar things you know or do to the transformation/upgrade it has new moves like its a bio-robot and now can shoot bombs and such. Silly Bosses My idea for this is that say you encountered an early on monster lets say equal to a terraria slime, well now this little critter say hops in your mech and now you have something weird like a small alien that you could easily kill in like your mech or a mech in general so now its like a tough challenge and possibly a handicap (if its your mech) this would lead to fun and intresting fights like a alien gets mutated and now its like out for revenge, this would have to be staged though or triggered by something advanced my example would be: Mech Upgrade as soon as you get it Boss B would jump into this mech and then you'd have to fight it, this would stop stupid things such as mech jacking randomly when you maybe just got your first mech or something. But besides mechas it could really be anything this is just my example of one.
