For me, even the bad episodes of season 1 have things to defend it. Not the least of which is because it's the first season and the writers and actors are finding the characters.
In a way, I don't think this is a fair contest. The season that should really be looked at with a cold eye is season 7. I think it had fewer gems than season 1. That season doesn't really have any excuses to be less than good.
I have to disagree. Finding the characters strikes me as excuse making. That's something that should be done before shooting starts. Twin Peaks, Star Trek The Original Series, Breaking Bad, Battlestar Galactica, Arrested Development, The Wire... all these shows were strong in their first season. For some of them, the first season was their strongest.
I think it's pretty plain to see that the problems with season one have little to do with the characters not being found yet. The writers commit mystifying blunders of basic rules of storytelling. A and B plots don't match up, episodes are missing entire acts, the stakes don't matter to anyone we care about, the main characters are not important to any resolution of the conflict... these are baffling mistakes for professional writers to make. The show got better when they corrected these mistakes.
And while I agree that season seven was a step down from 3-6, it was not without its excellent episodes. I don't think season one had anything I would call a gem of an episode. Conspiracy comes the closest. Season seven had Parallels, The Lower Decks, The Pegasus and All Good Things.