^JD, I might also be able to shed some light on your question. I'm an art director in AAA games development, and I've had hands-on experience with the types of things you're mentioning.
You guys are on the money with the prime issue being, well, money
. As with what was brought up earlier in this thread, anything that can share a 'skeleton' as we call it, can significantly reduce production costs, hence the proliferation of human-shaped aliens in STO. For a development team to create something that has a different body structure, it requires many things - planning, r&d, modeling, rigging, weighting, animating, pathing, and AI. A different body shape requires it to move differently, react differently with its environment, and also possibly requires a brand new set of movements - what we call an animation tree.
The other thing to note is that the budgets of said games might not be apparent to the end user, but those ones you mentioned are in drastically different budget categories. Assassin's Creed (Ubisoft), Red Dead Redemption (Rockstar), and Skyrim (Bethesda) are all massive projects being made by hundreds (if not thousands) of people, over sometimes 3-5 development studios split all over the globe. I would wager none of them has a budget of less than $50 million, and as much as $130M. I don't know the budget of Defiance, but if I would guess it's a medium-sized dev team of less than 200 people, and a budget in the neighborhood of $15-30 million. Adding a horse might be the difference between having one or two genders of main character, or even - when drastic cuts happen - between finishing the game or not.