First of all, I know you said you could not add another island or allow more habitats cause it would slow down the game. What about allowing habitats to hold 5 monsters each? That would allow 90 more monsters and would be very well received by the community.
Second, what if every time you bred monsters in breeding events, the odds of breeding a legendary increased? Or maybe instead of every time, every X amount of times? For example, I've bred the pair 5 times and now the odds go from 5% to 15%. I actually think this would increase people spending (thus buying) gems, because now people won't feel like they wasted gems when they don't get the pair as it just gives them better odds next time.