I think that the CD-ROM version of Space Quest 4 is the worst because it is just so buggy and full of timer issues, this really spoiled the game for me even though I loved the original floppy release.
I thought that Space Quest 2 was quite good even though the puzzles weren't that hard. I agree that is is somehow different from the other parts but that did not bother me at all. I didn't think that the locales were boring, I actually quite enjoyed making progress through the jungle. I also did not find the story any weaker than that of the other games, I mean, it's not like SQ1 or SQ3 had anything more to offer storywise. I'm probably biased because this is one of the first Sierra games I played (along with SQ1, PQ1 and Larry 1) , maybe I have to replay it because I just remember it as being soooo good!
The 'put gem in mouth' part sucked though, took me weeks before I figured that one out.