Mate, when Bill Jemas got Joe Quesada as editor-in-chief of Marvel, the stuff those guys put out for three years - I remember I felt like I was buying almost every comic Marvel was putting out. I was getting Alias, Amazing Spider-Man, all the Ultimate titles, New X-Men, Black Panther, Punisher - I pretty much gave everything a shot, and a lot of what they were doing was really exciting. Each title was completely self-sufficient (that's what the non-crossover part of what your talking about refers to). I remember, I'd be buying one Spidey title a month and getting all the stuff I need, whereas I dropped Superman when I realised I was buying two Superman titles a month, and getting only half a story. Really, the quality level on the mainstream titles was really quite high.
What was controversial was two fold - firstly, he and Joe Quesada got a lot of good talent into Marvel to do Marvel titles. He basically said to not care too much about what had come before but to just do the best stories they could. They got things like Grant Morrison and Frank Quitely to do New X-Men. This was really quite something. Basically, at the time, the X-Men books were unreadable. No one knew what the hell was going on. They were stories about other stories. It was so bad, that they realised that the X-Men movie came out, was a huge success, but no one was reading the comics. They set out to change that. Grant Morrison was at the top of his game having finished his run on Invisibles and JLA, and Frank Quitely was doing one of the biggest comics at the time, the Mark Millar-penned run of Authority. Quitely left Authority to do New X-Men. This was a big thing. And in three issues, Grant Morrison and Frank Quitely revamped the X-Men.
That's not all - they created the Ultimate universe which was a huge deal back then. They got the editor of Axel Alonso to clean up the Spider-Man titles - and he did; he got J Michael Straczynski onto the title and he did a great job on it at the beginning. They revamped the Hulk. All kinds of new titles were coming out, for good or ill: Marville, Alias - there was even the Epic series line. Not all of it was good, but there was just this feeling of new stuff coming out... that there was so much to see. It was a kind of near-reckless overhaul of Marvel that was so controversial. They got rid of the comics code and came up with their own certificates for comics and invented the MAX line to publish adult comics like Cage and Supreme Power.
It was just this incredible influx of creativity, and this total, "No more nonsense. We'll do anything, we'll get the work done, and we'll surprise the hell out of you each month" that was controversial.
But the second controvery sprang from this - Bill Jemas, so eager to just get rid of anything that wasn't working, offended a lot of fans. He would often come out and tell fans to grow up and (famously) get out of their mum's basement. He was very much not interested in pandering to the fanboy community that kept Marvel afloat for 10 years.
Basically, Bill Jemas and Joe Quesada realised that most comics were being sold to people who already bought comics and weren't selling anything to anyone else, so they decided to get people who weren't into comics into comics and that meant changing a lot. And if you didn't like/want the change, Jemas was candid about his feelings on the subject and went off and changed things more.
At the time, DC was completely at a standstill. Nothing was happening and Marvel was just pwning the market.
However, Bill Jemas' reckless pursuit for good comics did alter the franchises. This was what made it so exciting. But for Avi Arad, who was selling Marvel's licenses to Hollywood at the time, found it difficult to do so because the franchises would get altered and changed. He told Jemas to stop changing stuff. Jemas refused - I would hope because he understood that the Marvel universe was stagnant and milking the universe for franchises is poor long-term strategy. Avi Arad had him fired.
And ever since then, Marvel has declined into a quagmire. The Ultimate line is appaling, once great titles haven't changed but are now bland - Amazing Spider-Man for example. The most enjoyable Spidey title for me at the moment is Spider-Man Loves Mary Jane. Where once, we didn't get crossovers but solid titles week in, week out, we know have enormous crossovers that tie-in everywhere that aren't worth following half the time. The same writers pour out the same stories all over the place.
I think Bill Jemas, on his own, would be a reckless force of chaos, destroying titles left and right. I think Joe Quesada, on his own, is incapable of getting the best work out of people who work for him. But together, those two brought out the best Marvel comics era in my life time, I think.
I think that the guys doing the jobs now are trying to do the best comics that they can, I really do. But I also think that no one is pushing them to do the best, and as a result, they aren't.
Helluva shame.