Indeed, city of heroes had alot of it's best things on accident. The original developers definently never realized that, cryptic when they made CO really just did the same thing Ion storm did when they made deus ex IW: they never realised what made their original great game a hit(refering to deus ex). They listened to all the wrong people that had a very very narrow view of things. Then they never figured out or realized what city of heroes had, the devs that didn't touch CoX wouldn't have known that there were so many alternate playstyles.
Cryptic wasn't completely blind to what made CoH great when they made CO, but their original ideas I would characterize as trying to replace them with something else interesting, like replacing archetypes with a more interesting developmental system. The problem was they didn't possess the technical sophistication to pull it off, and ended up with a very flat open powers system. It was that flatness that killed replayability more than just the pure openness. They were experimenting with other ideas in beta, but for various reasons they fell through. I thought frameworks had promise, but at some point they just up and terminated the idea, I believe (but this is just my guess) because they realized they couldn't pull it off before launch.
I also think they learned the wrong lessons from City of Heroes, one of which was not that all these elements of CoH were important to making a strong casual-friendly game (global chat, ubiquitous movement, simple gear, etc) but rather that you can incrementally add these things over years and people will wait around for them. The notion that because MMOs are always in development so its not critical what you launch with is something you also see in the fact that they repeated the same mistake CoH made at launch: have insufficient content to level properly. They thought they could get away with thin content twice, but they were wrong. When CoH launched in 2004, there wasn't even WoW to compete with. In 2009 when Champions Online launched players were more discriminating and competition for attention in the MMO space was ten times higher.
I don't blame Cryptic for trying to be different. I can blame them for making the same mistake of having insufficient numerical control over their game (and thinking a couple of spreadsheets a proper systems analyst makes), thinking your players will give you years to screw around figuring things out, and focusing too much on outdated MMO dictates and not enough on the player experience in general.