I, for one, hope that FFG has learned their lesson in trying to bolt-on a concept for an already existing game that was not originally designed for the concepts in question. Trying to do this never ends well. If the game wasn't designed for the functionality to begin with, it rarely works out by adding it after the fact.
They are better off simply creating a D3e with that concept built in from the start.
Just my two cents worth.
I agree up to a point. While there are extreme mechanics that can drastically shift the functionality of a game that should probably be reserved for future editions (for example, I don't know that trying to create a skirmish mode for D2E such as is found in IA would be well advised,) one of the biggest benefits of expansions is to introduce new (albeit less radical) mechanics to the game on top of the new content. For example, the rumor mechanic first introduced with Lair of the Wyrm I think added a new aspect to campaign play that is very interesting. Similarly, the secret room treasure card, corrupt citizen cards, influence- all examples of new mechanics that are positive contributions from expansions. The threat/plot card mechanic is also a really neat addition. While you can argue balance of specific content encompassed by those mechanics, the mechanics themselves are good ideas that have (in my opinion) been implemented very well into the existing D2E framework.
The Coop adventures represent a much larger departure from the campaign playstyle than anything else released for D2E. I enjoy the coop adventures and am surprised by how they take the second edition components and put them to a very different, yet enjoyable use (had you tried to pitch the concept of a loot track or a doom counter to me I probably would have laughed.) Perhaps FFG has just learned to test things a bit more before releasing them?
Most of your initial points, while absolutely valid, are valid because the changes to the base game itself are minimal. Adding in additional "mechanics" or features such as threat, fortune, rumor, secret rooms, etc. all extend the base game WITHOUT changing the base game rules in any material way. That is why they work so well.
Even the Co-Ops really only extend the base game, not really change it. You still play by virtually all of the same rules, it just provides additional ones to automated the OL.
I also agree that a better comparison for D1e-RTL would be something like IA Skirmish mode for D2e. This would drastically change the base game, and would not, in my opinion, be able to work without changing the rules significantly. And thus, it wouldn't work real well.
When I think about D1e, and the hundreds of cards/items involved, and then the attempt to restructure all of the rules to make RTL, with additional items, dice, etc. I just shudder at trying to play test every possible combination/scenario.