Deus knew he had hardware he was locked into. He knew he would continue to need 'hardware', at least for as long as it took him to recompile and fully change from a single-site AI to a distributed-processing AI. The brain linkage tests in the Arcology were experiments to discover if human brains were capable of being reprogrammed at a sophisticated enough level to carry his decompiled code and, with sufficient numbers of them linked online, to reassemble him outside his prison cell -- the Arcology.
All of the other experiments -- armoring people up, making them quicker, etc. etc., and having the Blues use them for target practice -- were to ensure those brains' survivability. Remember that after every 'test firing' (i.e. Blues target practice), the shot-up victims were tested for brain functionality, and compared against their previous levels ...