The second season definately had some great episodes, particularly close to the beginning and end, the problem was the long stretch of episodes in the middle of dubious quality. If you look at my first graph you can see that the longest stretch of poor-average (0-5) episodes in season 1 was three, and it only happened twice, so you never had to wait a month for a good episode to remind you why you're watching the show. In season 2 those stretches were longer, and there was more of them, and when you're watching a show on a weekly basis that can get very frustrating.Although I've only seen eleven episodes of season two, I don't really see the drop in quality everyone else seems to notice - as far as I can see the first two seasons are pretty much the same, except that season two does have a couple of episodes that I really, really like.
Season 2 also had Precious Cargo.

In the TNG episode First Contact Picard commented that a disastrous first contact with the Klingon Empire led to decades of war. It should be a trivial thing, a throwaway line from an unimportant TNG episode, but the amount of times that I've seen people use this line as an excuse for why they don't consider Enterprise canonical is unreal.What continuity issues arose from the Klingons being introduced early?
The line doesn't bother me too much, but B&B could have saved a little bit of their reputation and the reputation of the show if they hadn't been seen to break continuity in the very first episode. And for what? The Klingons in Enterprise were rarely interesting, they were dumb and mean and very little else. The only episode I can think of where the Klingons were treated with respect by this show is Judgement, and even then only for one character.