Yes, it's the Borg and Q ones that stick out. I can't see why there'd be anykind of a vote for the Q one given that it's basically all of his episodes. Similarly with the Borg set, given that they could only do a certain amount of episodes, the episodes that ultimately went on it would seem to dictate themselves. I can understand why something like the Time Travel set or the Klingon set would require some sort of vote, and in truth, it's a great idea, we get the episodes we'd really want, well providing the ones you voted for won I guess! The Captain's Log ones were basically one choice for each Captain and then the rest were fan-voted ones, which again is fairly logical, however, I have to admit, some of the Captain's choices were disappointing. Patrick Stewart picked 'In Theory'. I know why, it was his directorial debut, but for me, I'd have preferred him picking an episode that he felt best showed off his character, or one that he enjoyed playing the character in most. Avery Brooks' choice was a fairly obvious one, but I loved that episode, and it's a great Sisko choice, so fair play. Similarly with Mulgrew picking Counterpoint, good selection. Bakula picked Judgement I think, which is a decent Archer episode, and then did Shatner pick The City on the Edge of Forever? I think it's just Stewart's choice that disappointed me.
Going back to the MU set, I think that if it were just marketed as a 'Mirror Universe' set then they should have stuck with the 8 episodes and reduced down the RRP. Nofan selection, but there wasn't with the Borg or the Q ones either, and given the narrow and definitive scope of the subject matter, that's understandable. Now that they're calling it the 'Alternate Realities' set though, then it opens up the fan-voted stuff again.
Personally, I think they should have had a Mirror Universe/Section31 set, although that would have just added more DS9 episodes!
A decent future release might be a Maquis set. TNG, DS9 and VOY could all contribute episodes.
Journey's End (TNG)
Pre-Emptive Strike (TNG)
The Maquis Parts I & II (DS9)
For the Cause (DS9)
For the Uniform (DS9)
Blaze of Glory (DS9)
Caretaker (VOY)
That would be 9 episodes, I'm sure you could pull a few more Maquis-centric Voyager episodes in to bring the count up to 12.