Paradroid is killer.
Oh, and I bet I could think up a ton of pretty fun improvements to the game. The real question is would you want to change up the formula at all? It might make it into an entirely different game.
For example, I could see a real benefit to really defining different components the droids have, and making that change very apparent in how you play. Legs, arms, eyes, etc. For example, for legs you can have wheels, treads, hover, etc., and make changing up your droid more critical to how you play, like spider legs can walk up walls.
Then a choice between hijacking an entire droid for a limited time, or trying to retrofit your own 001 droid with a different components. Make your 001 wear down and need to be kept up. One of your legs get blasted off? Well, hijack that maintenance droids wheels and attach them to your droid instead.
Maybe add some upgrade/ability expansion concept to make hijacking a droid 500 digits above your own a little more evened out. Like if you manage to hijack a 711 droid, you can't use it's EMP attack until your Paradroid is upgraded enough to control level 700 weaponry.
Then we can tinker with the concept that your paradroid has a human brain, so you have a very fragile organic tissue that needs to be protected. The stress put on your brain affects how long you can hijack other droids for, and how much time you have to perform transfers. Maybe a critical shot made on your brain forces you to eject, and the droid you hijacked comes back to life.
Having an element where the ship is flying towards to a mars colony or something to destroy the people there could add an element where you have to play against the clock, or have a need to hijack the ship itself to prevent it from accomplishing it's objective. Maybe you have to get to various decks to sabotage weapons, shields, hyperdrive, etc.