I've always wanted a game that took a formula somewhat like what is found in the Monster Rancher series and take it in a different direction. For a two sentence summary... Monster Rancher basically revolved around training one (or a small handful, never more than 5 at once as far as I remember) of Monsters and entering them in tournaments in which they would battle other monsters and get rewards and such for doing well. The Monsters did in fact age and "retire" but it felt a lot less jarring than other games that have tried such things because it was part of the formula. It was built around many generations and breeding successively better Monsters each time around.
Now, I enjoyed these games for awhile, but I eventually found the battling itself, which was meant to be the real "point" of the game to be the most tedious part of it. I enjoyed having a game that was geared towards many generations of monsters... maybe, to the OP, you could experiment with a system somewhat like this. You spend time growing and training some creature which will eventually reach a stage of maturity that allows breeding. The offspring would then evolve in some way (either by deliberate player choice, or by some more random factors) which would be determined by the way in which the parent creatures were brought up and trained.
Just a thought...
This is to some extent being done in current virtual pet sites. BeastKeeper, for example, has a somewhat tedious combat system by which pets are leveled up, to a maximum of 50, at which point they acquire the title "hero". The offspring of two hero pets gets an assortment of stat bonuses, and there are some quests only they are allowed to attempt. The pets can't actually be fought with before they are mature, so that part is waiting rather than actively raising them, but the game's still in beta and they have an open call for feature suggestions: one of the many feature suggestions so far is to add a minigame only playable with immature pets. I don't personally like this system, but you might want to try it out and see how it compares to your vision.