My choice would be 16:9 with minimal cropping. There are a few ways it could be done - CG to remove the lights and stands at the edge of shots, CG inserts to extend the frame where necessary, new SF shots (not too hard with extending the starscape background for space shots), subtly stretching the edges of shots and as a last resort, cropping.
Some of this would be expensive, but as digital tech gets cheaper it will become more viable.
This is one of my bug-bears about the internet. When people talk like CGI can just do anything
. "Yeah, y'know, whatever. We can just, like, fix it with with CGI. That'd be cool, right?"
Putting aside the matter of resources (CGI still ain't cheap, like you say), I don't think it could be convincing either. Especially not when you've got a physical set that was made in 1986 and you're trying to blend it with 20XX technology. I've yet to see quantifiable proof that this can be done convincingly enough to look like an actual, real set. It'd just plain look weird