1) Communication & distance.
It's not so much distance, or public order problems, though those should become restrictive. It's more that money becomes a non-issue, and therefore distance becomes a non-issue at well. This can almost not be countered (since money growing linearly or even as a root function is a problem in any strategy game), unless you simply want to halt player expansion after a certain number of provinces (which sucks if you can't get your goal, and if you can what is the point?). That is not cool.

Note that CA are trying to simulate distance by restricting cities to money, and castles to troop building. But distance will only delay the inevitable, unless attrition due to travel is high enough. And both make the mid/endgame only more tiresome, instead thrilling and fast like it should be.

2) Integration.
Is nice, and adds flavor, but if you have 50 provinces, and you have to perform action X or Y to assimilate the population, that means a lot lot lot of micromanagement. That is not cool.

3) Civil Wars.
That IS cool and MTW kind of had these with Factions re-emerging. Imagine a faction re-emerging while half of your empire is turning rebel. Each rebel province has a chance of joining the re-emerging faction. Suddenly its the England-France 100 years war all over again!* Hurrah!!

* You do want to eventually win though, so Civil Wars should be dependent on chance. Sometimes they happen, sometimes they don't.

I would rather see a system in which the player could only raise a couple of armies (1 to 4 at the max depending on size and layout of the kingdom).
This idea is used in Shogun the boardgame:
http://www.boardgamegeek.com/game/221

And it places restrictions on the number of units you can put in 1 province, unless (one of your 4) an army is there. It would greatly improve the campaign map AI, and greatly reduce micro-management. But at the cost of freedom. I cannot see CA doing that, even if i like the idea.

But then TW wouldn't really fit anymore in the RTS mould of techtrees and unit/building queues.
Sure it would. The recruitment system would change however, to one of recruiting at one central place (the army level) instead of recruiting at each individual city. See for example Heroes of Might and Magic, where armies can drain a city of all its troops. They still have to visit all your cities though, which should be replaced by a reinforcements system: Everything you buy is simply sent to your army without appearing on the map. The time it takes should increase with distance, up to a maximum. That would reduce micro-management lots, but also reduce realism. I'm afraid you can't have both.

CA's distinction into city/castle already makes an attempt to reduce the number of spots where you can/have to recruit from.

May I add:

4) Being able to start in a mid/late era, reducing time and provinces while increasing tech.

CA have already added:

5) Protectorates. Hate them you may, but these babies do speed up the mid/end game, meaning you'll actually finish. Though I think protectorates should be more definite, actually handing full control to the conqueror.