It seems that I've given so many summaries about where I think this show went wrong, I may as well be paid by the mile for it. Let's see if I can do so again without cracking that 20k character limit for a post.
Panthro, as usual, summarizes the problems well. I feel that this show was written as a bit of a release after having to buckle and compromise with Kid's WB with "X-MEN EVOLUTION" about what couldn't be done. Apparently the creators had to haggle with the network for a lot of things, and many things they wanted to do had to be scrapped, or delayed, or so on. One major network caveat was a focus on the teenagers, which was why Wolverine was marginalized (although he still got more focus there than, say, Storm). So to me, when the chance to do "WOLVERINE AND THE X-MEN" came aboard, many of the same writers and producers found themselves with the chance to do whatever they wanted on an X-Men show, with whoever they wanted, with likely the one corporate stipulation that Wolverine had to be the lead; which, frankly, I don't think bummed anyone at the office. There seemed to be a rush to do everything and anything, to cram in a million cameos, to do that deep, complicated and mature story, and have all the big explosions and gritty suspense that Kid's WB wouldn't let them do until about two seasons in. The problem, besides the execution, was that the characterization suffered. Even Wolverine, the star attraction, suffered a bit from the premise. He was often removed from where he was ideal, and sometimes came off like a standard gruff, hypocritical general. Storm was a non-entity, and Iceman not far removed from that status, too. Beast actually had a fun rapport as "co-leader" at the start, but that ended as soon as the roster hit about 7 members. I could probably write a full thesis on where Cyclops went wrong. Shadowcat and Forge could easily steal scenes or chew up scenery, but even they rarely escaped cliche. Nightcrawler was probably the best handled of the X-Men, and even he took a back seat by the time the endgame approached. Rogue also had a good subplot for the first half of the series, but after she rejoined the X-Men by the middle point, both that and her general character seemed to be lost to the void beyond showing up for a fight or one blurb at the finale.
Emma Frost was written as a tragic figure, and an anti-heroine. Most of her arc was intertwined with Cyclops, to the point that neither of them were quite as engaging alone (although Frost could still provide cute banter without Scott, while Scott just sulked if alone).
The villains probably fared better. Magneto I thought was handled pretty well; he had more of those anti-hero qualities that the 90's 'toon Magneto had, while still having the menace that the Evolution Magneto had. I liked his complicated relationship with his three children. Scarlet Witch and Quicksilver were handled well, or at least were interesting and usually consistent with who they were portrayed as. Even Lorna had her place. Senator Kelly was also handled well, and it was a treat seeing Mister Sinister again, and the Marauders.
As for the X-Men? To be blunt, after one episode, I probably liked Rover more than about half of them. And that's a problem once a fight comes in. By the finale I found myself just so disengaged with the fates of many of the characters.
The execution of the show was hit or miss, and I think that the show wasn't able to properly execute the ideas that the producers had, and while some areas went too far, others didn't go far enough. The producers intended for this show to have an X-Men who weren't in lock step because Wolverine wasn't supposed to be the best leader. The result was an X-Men that was still lock step, and beyond an occasional wisecrack from Kitty or Frost, none of the X-Men ever questioned Wolverine; no, not even Storm. If anything she was the quietest of all. Even when Wolverine was flat out wrong or led the X-Men into a trap or a misstep, or barked at Cyclops for doing a loner vengeance crusade before immediately doing the same thing himself ("because I'll survive" is his excuse; by that logic, Superman should yell at Batman every time he does something alone, yet smash through walls on personal vendettas in Justice League), none of the other X-Men seemed to care, and that harmed Logan too. On the other hand, the producers wanted a "flawed Cyclops", and with they they overdid it a bit much to produce a Cyclops who could hardly get out of bed or shave, or was never worthy of being a leader or even of Jean or Frost's devotion. The audience was told that this was out of character for him, for him to be a selfish, aggressive incompetent, but in his origin episode, it seems he was this way all along. The end result is Wolverine didn't replace a leader; he became the leader of a team that never seemed to have one. And even that was a sham, because Xavier was still the one giving orders and guidance.
Professor X was another flaw of the show. The producers stated they had a dilemma, because they didn't want to kill or permanently remove him, while they also didn't want him being present all the time. The compromise they devised didn't work. The result was Xavier was still the one calling the shots, and in theory any X-Man could have just carried them out; he was simply gung ho on Wolverine, to the extent that none of the other X-Men mattered. If Wolverine was having a conflict or personal doubt issue, Xavier would make sure to spend his rare time travel psychic time to soothe him. If Cyclops needed it, he was on his own. When it came down to offing Jean, Xavier suggested it without a moment's hesitation. It got to the point where it was hard to disagree entirely with Marrow in the future; that the X-Men were just Xavier's pawns, and he just wanted people to follow his orders and didn't actually care about the consequences. To be fair, Xavier had these moments in the comics (at some points resenting that Cyclops and Jean chose to actually have a private life when he abandoned it for the cause), but none of this is treated as a big deal. The X-Men were also quick to turn on anyone who was being brainwashed or possessed...except for Wolverine. Nightcrawler had to take GREAT care to not simply batter him into submission when Mojo was controlling him. Even when Wolverine's personal enemies came to the Mansion's doorstep and could have killed the entire X-Men if they chose, none of them complained. The only one who seemed to was Cyclops, who was always eager to blast Logan, but due to overdoing his flaws, he usually came off as a demoted spoiled brat.
Even the precious season long storyline that was almost the sole purpose of the show was a little fuzzy. It sought to intertwine the Sentinel plot with the Dark Phoenix plot, when none of them had anything to do with the other. They both simply came to a head around the same time. The Sentinel plot was what drove most of the series; Dark Phoenix seemed to come into focus just because the producers were nervous about their finale relying on robots, so they figured to go with a classic. As such you had Master Mold basically being dispatched with by 2/3rds in while the Phoenix plot came to the fore suddenly over about 4-5 episodes. True, the Future Team fought her, but they're in the future; it was the past that mattered. Magneto led the Sentinels at the end, but that was mostly to keep everyone busy with explosions. What, I wasn't supposed to notice?
WOLVERINE AND THE X-MEN was a frustrating show. Like a lot of the Kyle/Yost/Johnson collaborations, it mixed moments of brilliance in with moments of mediocrity or sheer incompetence or wasted potential. There were moments when it captivated you, and moments when you wanted to throw up your hands and give up on it. If you were a fan of Wolverine and adult X-Men and care more about action and plot than characters, consistency or sense, it was a fine show. To use a sports cliche, it wasn't a complete game. It wasn't the sum of it's parts. It often distracted itself with mistaking the trees for the forest, and working on making pretty trees while missing the grander point. I suppose over-ambition is one way to put it. In retrospect some could say this show played out very much like a first season, and a second could have taken this experience to iron out the flaws better. But of course, now we'll never know, and it has to stand alone.
Although I will tear my hair out of a third show teases me with Colossus and then does absolutely nothing with him.