IIRC, Janeway and Chakotay never hitting it off pissed off legions of shippers.
I've also recently noticed that many fans were dissapointed in TPTB for giving up on Worf/Troi. Same probably goes for Picard/Crusher, even though they got married in post-NEM novels.
I for one was pretty dissapointed when Seven picked Chakotay instead of Kim, and I still think Riker had more chemistry with Ro than he ever had with Deanna.
What are your favorite couples that never came to be?