Which bosses were made easier for the Genesis version? I'm looking at my damage tables right now, and I'm not seeing any values that were increased except Guts-Dozer taking a little extra from fully charged Atomic Fire. In fact, a few numbers were decreased on the bosses' end: You know how QuickMan and FlashMan took 2 units of damage from the P-shooter? Well, on Megadrive they only take 1! You have to shoot them twice as many times! Invulnerability flashes also last a little longer, so you can't beat anyone as fast, and you can't get as many extra hits with the Clash Bomb.
FlashMan's shots do only 1 unit instead of 2, though, but that's because all the Generic Yellow Enemy Bullets were changed like that. Now, if you're talking about the bosses' movement patterns, that could go either way.