it can be done well. off the top of my head, a couple good examples are south park and marvelous misadventures of flapjack

That's why you have it done by an actual animation studio with actual artists who can redo the composition if necessary. Way easier to do with animation than with anything else, technically speaking, e.g. you can crop out characters, reconstruct the matte and move the characters elsewhere without having to account for fancy realistic lighting.

The alternative is to be Babylon 5 which was shot on 16:9, framed for 16:9 but making sure a 4:3 crop doesn't cut away important bits, in anticipation of the new format, alas the CGI was done in 4:3 and quite low res and noone has ever bothered to prepare a proper 16:9 release (and with the remake on the horizon that ever happening becomes more and more unlikely). There's a version out there in acceptable 16:9, though: Most of the footage doesn't include CGI and so is fine as-is, arguably better than the 4:3 crop, and the panned/zoomed CGI parts aren't too jarring. Definitely blurry, though. I'd actually recommend it over the original release, imperfect as it is.