Why is it so rare? Because its really bloody hard to pull off even close to convincingly!

From the day we're born we study faces, learn all their little movements, "micro expressions", small muscle contractions, skin stretching or jiggling in certain ways, etc etc, that are there all the time, but we're not looking for them normally, as soon as they're not their tho, we know something isn't right. All that makes it very nearly impossible to animate a truly convincing CGI replacement, the best ones to date have all been facial mo-cap with CGI over the actors face. I say "very nearly impossible" because, I don't want to discount the possibility of someone taking two years to animate a 5 second clip frame by frame to get every slight detail, but its not going to be cost effective or practical for any project at this point.

It would also help to define what you're looking for, and where you draw the line. Do you count stuff like Davey Jones et all in the Pirates of the Carribean movies? Maybe not, but there's not much left of the actors face by the time VFX is done with the footage. Gollum in the Lord of the Rings/Hobbit films? If you want total replacement, what about Alita in Battle Angel? Not exactly a "natural" human character but a total replacement and a pretty well done one at that. I suppose we could mention Avatar, but, ugh, I'd rather not, not CG's finest moment. 

Total CGi character replacement has been done a few times, first one that comes to mind was Peter Cushing in Stars Wars: Rogue One, which looks pretty convincing, but you can tell it offs, a lot of the movements aren't nearly as "sharp" and tend to "drift" some, and the skin is kind of stiff, especially in the cheeks. Paul Walker in [at least] one of the later Fast and the Furious movies. I'd recommend checking out Corridor Crew's videos on this topic.

https://www.youtube.com/watch?v=2ZKPnuUFwOk

They have a few others, that get into "deep faking" as well [ https://www.youtube.com/watch?v=861gfPVmgdc ], which is the direction that things are more likely to go. Seems like that's giving more realistic results at the moment, than a full CGI replacement is. I'd guess we'll eventually get to a point that its a hybrid of the two methods.

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