My picks would be Supreme Commander (has a slight hint of the C&C DNA, but very different resource management, you can still sit in the base though and build an army, the resource model is more akin to C&C generals, then base C&C
Grey Goo which is made by some of the people who made C&C might be worth looking into
Total War Warhammer, is an odd one I might point to, see it IS a total war game, but it has a lot of different aspects that you don't find in the base Total war games, and I find it the best total war game they ever made (With Shogun 2 being the runner up).
You did not ask for it, and in a lot of ways it does not really fit what you are looking for, but Company of Heroes 1 is cheap nowadays, it still has base building and such, but it is more a game of holding key points out in the map, then the base. So I would only look at it if there was nothing else.
Oh, and if you have not played it, C&C 3 and its expansion were REALLY good C&C games.
Starcraft 2 has a free version, it is somewhat basic, but since you liked warcraft, you can download it and see if it is a game you would want to play. It has some pretty darn good SP missions and skirmish is fun.
Act Of Agression is very close to C&C aswell, it has some slight polish issues, and a few aspects I do not like, but it also has most of what you ask for, as far as I know, it was made with Generals as a role model, it is a fairly good game.
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