With Shadow's A.I. for allied groups, it would actually be terribly exploitable in how it works. For instance: say there's a LARGE swarm of Dark Arms aliens ahead. If you switch to dark allied mode, they wouldn't attack you, letting you skip them. Same with G.U.N. troops if you switched to hero around a large contingent of troops and mechs. It'd make some of the final levels in the story branches utter jokes since you don't even need to be aligned with a side to complete that specific mission.
On Sonic Colors itself, there was a magazine article someone posted on Sonic Retro that said for the most part, Sonic Colors can be played and likely beaten without even using the wisps, should you choose to. Chaos Emeralds, as always, will be present too.