To this day, I actually don't know how three people would get in and out of the ME1 MAKO in the first place. I always felt that the vehicle was a bit small for 3 people. Especially the height, I mean, did they lie down in there?
So, if there would have been an animation, it would probably have taken forever to watch all three people squeeze in and out of there. 
If there would be an animation in the next game, I''d hope that it's very fast and unobtrusive. I certainly don't want to sit around waiting for a few seconds every time I get in/out the vehicle. In that case, I'd rather go with the teleporting again (which didn't really bother me that much tbh).