There was a big disconnect from the family feel of the franchise for a while before Morrison came along. I remember hearing the complaints when they did the "unofficial" first Schism that took place prior to the Twelve event. Morrison gets the blame for stuff that really shakes my head sometimes.
That's not really true. The break-up prior to the Twelve was staged by Xavier and Jean to root out who the infiltrator was and they were back together come the Twelve. It was just a plot point, not a perminent status quo. It lasted a grand total of 4 months I believe. After that they were good again until Morrison completely scarred the franchise with his treatment of Scott and Jean.
It was a second mutation and a sweeping effect that went through half the mutant race. The only ones still noticed by editorial and the general populace are Beast and Emma. Personally, I prefer feline Beast. It visually reminds me of Ron Perlman from the Beauty and the Beast tv show back in the day (with Linda Hamilton). When an artist does it right it looks terrific....the downside.....it's done wrong, he looks like a friggin donkey.
Oh I understand secondary mutation, Morrison just pulled it out of the blue with no build up. Heck, he didn't even mutate Beast. He was just suddenly cat-like.
That said, I don't mind secondary mutation. I just think Morrison handled it poorly.
Why, because 7 years later Marvel still runs with some of his ideas and builds off it? By that logic we can totally bring your hero Bendis into this...
Long term plot points isn't bad. I actually prefer that to this crappy "new reader accessable" thing Marvel seems to cling to. It's when you completely crap on something that's been an icon in the industry for 40 years... and then follow it.
And you act like I think Bendis is an amazing writer or something. I doubt he'd even be among my top 10.
Like I said though, I loved a lot of what Morrison did. The only thing I dispised, and in my opinion it tainted the entire run, was his handling of Scott and Jean. That's it. I loved Xorn, John Sublime, Planet X, Riot at Xavier's, Fantomex, etc. But he tore down Scott and Jean's characters "to make them interesting" like cheating on your spouse is somehow more interesting, and then he killed Jean and hooked Scott up with Emma comletely destroying any chance of recovery.
I honestly wanted to drop X-Men for the first time in around 10 or 15 years at that point and honestly sorta wish I had. I've not really enjoyed much of it since. Scott's dropped from my favorite X-Men to one of the most bleh. I can't stand Emma even to this day (I never cared for her but Morrison made her detestable for me). I hate Beast's constant jadedness. Wolverine's teenage-girl pining for Jean has reached an all-time intolerable high. Xavier's been tainted multiple times. Banshee and Nightcrawer were killed off. Most of my favorite aspects of Morrison's run have been done away with but every single bad one's still intact and running. And tons of boring writing.
The X-Men are realy a mess and it just keeps getting worse every year and it's entirely due to the feel of the book and how far they keep removing it away from the family feel it had until Morrison took over. If not for my love of the characters I'd be saving tons of money.
That's why Wolverine & the X-Men was such a joy for me. It actually captured the feel of pre-Morrison X-Men. I don't even much care to read Uncanny X-Men now (though I will because I can't stop reading core X-books).
There's plenty of hate, especially since the guy has been overused as far as always showing up, but then when he is used, not much happens beyond him charging in and getting blown up, melted, tossed, sliced and or diced and pounded, just because the writer knows they can do all that without him dying. 
