1. CGI characters are way, way, way more expensive than live actors.
2. CGI characters are more difficult to film than live actors (this introduces a host of other complications, e.g. it is harder to use them for marketing of the film because many of their effects won't be done in time for trailers; "reshoots" are impossible; spontaneous improv on the set is much more difficult; a director might not have enough experience filming extensive CGI; the CGI might look shoddy)
3. Not all actors are willing to work with their faces obscured. It's not a coincidence that Peter Parker's mask either gets torn or he takes it off voluntarily in 5/5 Spider-Man film to date, that we get in-helmet shots of Tony Stark in every Iron Man/Avengers film, and that Wolverine never wears a mask. Now, you might still be able to get the actor you want if you offer enough money, or the role is juicy enough... or you might not. Do you want to take the risk?
4. The reason for the above is that it's difficult for a human (or animated character) to be dramatically expressive without their face. Fangface Mileena will always be stuck in one-dimensional mookland because we won't be able to sympathize with her. She can't smile, she can't frown, she might as well not have a mouth to emote with. MKX face Mileena? She can go in all sorts of directions as a character. Good, bad, worse, you name it. Storytelling opportunities open up to her.
5. This is all assuming an A list budget. What if it's a TV series or a webseries instead of a Hollywood blockbuster, like MK Legacy, and the budget is considerably smaller? We've already seen what happens - we get a Mileena who looks nothing like Mileena. That hurts character branding, because Mileena isn't a household name.
These might be completely non-issues to you, and some of them might never come up for the production companies involved, but you better believe that there are people at NRS whose job it is to think about this kind of stuff and make sure that all sorts of doors remain open to the franchise.
