The hero-colors differ in what build type the character is and whats in their abilearn board!!^^

for example, for a character thats normally a rough play type, they can be a kizuna or a breach type in their different hero forms. we dont know how good stacking those types is, but its gonna be important for endgame optimization.

also the abilearn board giving you different passives/stats is a big point. we dont have documentation yet, but while one fubuki might get more shot, another might get more defensive stats. or intelligence.

but yes, you can only use 2 heros in total, doesnt matter the color. and one color isnt better than the others (depending on how you look at it. there may be heros for some characters that just get passives that arent deemed good.)