I think I would make the game in a way that there would be multiple outcomes based on the choices you make. For example, what factions you support. There would be multiple territories on the map with key spots/elements these factions fight over. During your gameplay you would have opportunities to support one faction over the other (by giving them key items, or by specifically breeding certain types of monsters or monsters with specific attributes for them), or you can stey neutral towards them, but it might cause unexpected (and maybe detrimental) results later in game.
That's an awesome concept!
But...
You do realize that in order to get anywhere near the level of quality and consistent art design Breeding Season possesses alongside your suggestions, the game would not only have to be built with this in mind from the very start, it would require even more effort and time than what Breeding Season and Cloud Meadow has had poured into them put together, right?
What I'm trying to say is, it's not really feasible for a small indie team to make such a game reach a satisfactory full release.
I mean, it sounds really cool, and if a large enough team with plenty of funding and a neverending dedication to make it a reality was developing it, it might just work out.
But game development is freaking hard (not that I know from personal experience, I haven't gotten started yet, but I hang around a few devs and coders) and the more features and gameplay elements you add, the harder it becomes to keep a consistently high level of quality throughout the game, as you need to properly integrate all of those features into it.
If you have a multiple choice system in place, those choices all have to be tied into all other relevant gameplay elements, for instance economy, market supply and demand, NPC opinions, etc.
If you have a dynamic faction system on a world map, one which you as a player can influence, you need to account for every potential outcome and tie that into the rest of the game, so you don't end up with what is essentially two separate games with little to no impact on eachother.
In short, your idea would be awesome to play, but insanely hard for a small development team (especially one that hasn't secured plenty of funds up front), let alone a single dev to actually produce.
Most likely you'll end up with an abandoned game containing multiple half-baked features, and severely mentally exhausted developer(s).
I'm sorry to rain on your parade, but I've had to learn the hard way that game development is a lot more difficult than the Dunning-Krueger effect causes people to assume.
Edit: Shit, did I just lecture a game dev on game development without realizing it? My bad G.