I am full of bad ideas.
Remove evolutions, add experience points to the game. Want to get those slots? Have fun grinding recycler and grunt kills for that delicious exp. Sorry pacifists.
Add classes. Now you can finally be a level 5 cogmind priest. What's better for taking on the big bad in Command, a high level cogmind barbarian or a multiclassed cogmind rogue/mage?
New branch whose rewards can only be obtained by solving the RiddleBot's conundrums. Riddles procedurally generated each run.
Replace all sentries with behemoths.
Replace all swarmers with imps.
Add mimics: robots that look like desirable items until you step onto them, at which point they spring to life and attack.
Give Cogmind a love interest.
New unauthorized hacks that let you prank call Command.
Pay to win. Paypal over a mere $1.00 and instantly reset core to 100.
Merchandising, merchandising, merchandising: plushy versions of Cogmind 'n friends.
New ending where you sit all factions down and work out your differences through constructive dialogue.
New ending revealing that all events were Zhirov's dream after a night of too much vodka and seafood on the Cetus.