I have to say, I didn't much mind the yucky stuff inside Stellar's body. Perhaps I was conditioned to disgusting scenes, after years of playing Dragon Age: Origins (e.g. the Deep Roads), as well as Tales of Monkey Island (where you start one of the chapters inside a giant manatee. Don't ask.)
There was one scene that I thought was disgusting (and, alas, one you can't skip) - the bit where Roger rides the tapeworm down Stellar's digestive tract. I know that's a reference to Dune, but still ... ugh.
"Stooge Fighter" was a funny idea and a neat reference to "Street Fighter", but the Endodroid was ... disappointing. We've already met his cousin, Ah-noid, in SQ3, and the Endodroid has very little to offer in comparison.
One last observation on SQ6: the disappointingly small number of deaths. I think I died maybe 3-4 different deaths in this game, compared to 20-30 in other SQ games. That's not enough! We demand more ways to make Roger die!
So what did you think of SQ6, hmm?
(Incidentally, not sure if it's been mentioned before - but Gary Owens does a superb job as the bored narrator.
Plus, of course I loved the dysfunctional "information superhighway", and the Windows 3.1-like office... complete with Sis Inny...)