Yeah, the new color mechanic sounds good.
Just be sure to differentiate your colored bacteria from Dr. Mario viruses.
I'd like to see the colors correspond to specific abilities of the enemies. E.g. one color has spiky enemies, another has hopping enemies, another has floating enemies, etc. This would also go a little way for the colorblindness issue.
I look forward to seeing how this goes. Here's another small idea: Special colored platforms which only support you if you have the right color collected. Functionally, they could be similar to colored doors, but you could also think of platforming puzzles involving mixed colors and multicolored platforms.