Well, others have mentioned a lot of this, but here's my two cents anyway:
1) The Temporal Cold War. Not so much the concept itself, but the fact that it was so badly executed. It would have worked so much better, I think, if it had been a war between two possible alternate realities.
2) When it came to showing the rough and tumble early days of space travel, they lacked the courage of their convictions. For the first two seasons, especially, it felt way too familiar, and waay too safe. Season 3 and 4 corrected this, but many people had already given up.
3) #2, but times a factor of three when we're talking about the technology used in the show:
- "We have a transporter, but it's in the early stage" (effect of being in the early stage? One guy gets some leaves stuck in his skin in one episode.)
- "We don't have phasers, we have an early version called "phase" pistols. (Ah, you left off an "r." Wow. Balsy. Yet somehow, they work exactly like phasers.)
- "We don't have photonic torpedoes yet, they have photonic torpedoes. We get to see the early version." (An extra "ic." Again, stunning difference there. And how is it dramatically interesting to see "the early version" of something, when it works exactly the same way?)
- "They don't have shields, they have hull plating." (Which goes to 60% when hit, then 30%, then 10%... need I say it again?)
4) Resistance to expanding on what was already established in Trek's background. Why create the Xindi the Delphic Expanse, when you already have the Zenkethi and the Typhon Expanse sitting there waiting to be expounded upon? In order to do a prequel justice, you have to be the sort of person who loves to fill in the blanks with interesting stories, who goes to the encyclopedia and asks, "Is there anything already established that I could use here?" Again, Coto got it right, but sadly he was given control only after the show's fate was already sealed.