I 100% agree with you that custom content is better than random generated missions. However, creating custom content (especially in an MMO setting) can be daunting if you choose to continue doing so.

COH which you've mentioned in your post is a game that I personally believe could USE a mission generator. The quests they have, feel like they've been built randomly. And unfortunately they have the feel as if they are just adding in additional touches instead of truly unique quests.

However I'm not really into the discussion of Pregenerated content vs randomized content. I do not believe it is possible to replace content with randomness.

As for plot and canned script mismatches. I agree that this can be a problem. However, I doubt its a large one that is a big game breaker.

The player doing "the same thing over and over" is correct. But this is true reguardless of whether or not you're using custom, or random content. It is up to the developer to build a system that is robust enough to keep players interested.

Also, I stated before, that no mission generator should ever be considered done. Just like you should have a team that continues to update the custom content, you should have a team that continues to update the random content. However the bonus to that is for every custom quest you finish, you get 10-100 or more random quests.

I agree that most random generators out there are not that great at the moment.

Look at Anarchy Online. It has one of the better random quest generators, but it has serious flaws.
1. Map locations...I think there are only about 5 or 6 random map tilesets to choose from.
2. Mission types...Again I think there are only 10 types of missions, and combined with the map styles, you esentially end up doing the same thing anyways unless you're trying to mission blitz.
3. All in all it lacked a lot of variety. But I think that was due to lack of continued effort on increasing its options, not lack of a solid design.