Most of my complaints about the show have been covered here, and I certainly wasn't shy about stating them when the show was on, but, given the chance:
1. Executive blindness - ENT was a sad victim of its creators trying to have it both ways, to "do something new" while simultaneously (or "actually") trying to evoke, invoke and outright plagiarize everything they felt was most recognizable from the series with which they had most recently been involved. ENT had a fatal case of "Not Invented Here" syndrome, in that they seemed to actively ignore or prevent any outside perspective or creativity in the creation of the series; the designers were the same, the writers were the same (and when they weren't, they clearly had no idea of what they were writing), and the Beebs themselves seemed constitutionally incapable of seeing the flaws in their own stories, and compulsive about making sure that no one else's story got through without them recasting it in their own flawed vision. The design of Akiraprise is just a symptom of all this - they approved a barely-changed version of a ship which had known fan appeal, rather than trying something new and maybe even a bit uncomfortable. The problem is that, in trying to make ENT 'comfortable' for the existing fans, it actually felt more like 'sloppy seconds.'
2. Amateurish writing - I'll go to the end stating that the first two seasons had generally good ideas, ruined by lousy execution, and that goes as far as the Beebs literally 'executing' any good idea they had, and leaving it to rot in the sun. The Xindi "arc" was no such thing, being instead a multi-part story with muddled and unclear chapters masquerading as episodes - an arc is nothing more and nothing less than a secondary premise - not a story in itself - in which other, stand-alone stories share both the overall premise of the series and the secondary premise of the arc, but can still frequently stand alone. The Xindi season was nothing of the sort, so in general, its episodes were usually incomplete. On top of that, they were poorly crafted, as well, not only in their stories but also in their visuals - somehow, ENT managed to slip far downhill from the standards that its predecessors had achieved, which only made good stories that much more vital, and that much more obvious in their absence.
The 4th season was, IMHO, ENT's (and Trek's) worst, for the same reasons. Here, the series truly became nothing more than "Behind the Scenes of Star Trek - (subtitle: Everything You 'Know' is Wrong! - Because We Said So!)." The story ideas were about on par with most fan fiction, concentrating primarily on telling stories about other stories, or 'fixing' the gaffes that the Beebs had needlessly committed in the previous seasons. Like the rest of the series, the plotlines were irregular, as were the characters, and what little science was even attempted was laughably and transparently wrong - generally, they tried to replace the necessary elements of storytelling with technobabble and justplain babble, which leads us to ...
3. Terrible characters AND terrible casting. Let me first say that ENT had two stand-outs: Connor Trinneer and John Billingsley. Somehow, they usually managed to make whatever drivel they were given sound like it meant something, both in general and to their characters specifically - they created and delivered characters far greater than their material, and they did it consistently. Kudos to them!
Bakula, OTOH, took a bad character and made him infinitely worse. The befuddled approach worked for Quantum Leap because Sam Beckett was befuddled! But Jonathan Archer was supposedly the best Earth had to offer - you;'d never know this from either Archer's petty, insipid approach to everything, nor from Bakula's perpetually furrowed brow and seeming inability to deliver a performance with any subtlety or believability.
Blalock was simply a wooden, whiny prop - just because she was supposed to be unemotional doesn't mean she had to be utterly devoid of any connection to her material.
The rest were also props, that the writers moved around to toss lines on in any given script, but never really expected to deliver, and so they didn't. And poor Anthony was made a complete joke; at least Checkov was a funny joke and not simply pathetic.
And, of course, I could say that if you don't like episodes like "Cogenitor" or "Dead Stop" you are not ever going to understand what others like about the show, but I don't think this kind of statements has any sense. 
And TNG isn't made of awesome either, it's aged as badly as ENT has for me. DS9, on the other hand, while it has some real stinkers, is mostly good, including its first couple of seasons IMO.
