It seems there is a difference in quality between episodes, although they are all quite impressive. I noticed some grain on the first few I watched randomly. But I just finished watching “Where No Man Has Gone Before” and it was stunningly clean and sharp!
In contrast I also just finished watching the first two Godfather movies and they are just about the worst quality blu-rays I have ever seen. From what I've read that was intentional. Supposedly. So you just never know what you're getting. Still I would rather have them as they were meant to be seen and not put through some questionable software alterations.
I wouldn't hesitate to buy the TOS blu-rays if the original poster is still debating, as long as the price is reasonable.
You read wrong about The Godfather. The first two films were painstakingly restored by a team including one of the absolute best in the business, Robert A. Harris (who also worked on the stunning Lawrence of Arabia restoration that was released last fall). The Godfather films on Blu-ray are about as close to the original films as are likely to get. The goal was to match an original dye print (held by the Academy of Motion Pictures that awards Oscars) and by all accounts, it was a rousing success. If one has only ever seen them in previous home video releases (laserdisc, VHS, earlier DVD releases, cable or broadcast TV), then the blu-rays might not appear as one remembers--but that is not to say they are not as faithful to the original as they could be. You may not like the way the restoration looks (that is entirely your prerogative) but they are not a radical departure from the original intended look. Quite the opposite, in fact.
If you want to see a film whose Blu-ray release dramatically alters the original, get a hold of the first Blu-ray of The French Connection (the most recent release, after much outcry over the first one, is about as close to the original theatrical prints as it gets, as well).
As to TOS on Blu-ray, the non-effects stuff looks dramatically better than any previous release (sometimes TOO revealing, as they were never intended to be viewed by the audience at such a high resolution). The original effects were not designed to hold up to theatrical standards of the day, let alone now, so it is understandable they look worse than on lower resolution sources.