If Relic or Westwood couldn't do it, what hope did the little guys have?
There are some RTSs here and there but hardly with any effect
Adventures, turn based games and RPGs are kinda alive with some indies and shity AAA titles but RTSs are near extinction. Innovation and style of older games died a horrible death.
I feel that the problem comes from the genre itself. I bet quite a few indies would like to make an RTS.
But those games are quite possibly the hardest to make.
You can't just take any engine, as RTS games have to be well optimized or they will suck. There is one RTS engine out there, but... did you take a look at it? It seems very limited to a very specific kind of RTS, and I don't think it comes with a good editor, etc.
While there are ready-made solutions for pathfinding in turn-based games or games with few actors at once, there is absolutely nothing ready-made for pathfinding that could handle dozens or even hundreds of units moving in a somewhat intelligent fashion, avoiding obstacles, finding alternate routes, etc. Proper pathfinding, as someone who dug into it myself, is IMO the biggest problem. Because it HAS to be really well-done or the game will suck.
Then you've got the AI which really shouldn't be bad and it has to be quite complex, too.
Add to that all the assets that you need. Nobody will play an RTS game with just one or two races. Doesn't matter if 2D or 3D, you need A LOT. And that costs a lot of money to make.
And finally, you have multiplayer. Integrating multiplayer about doubles the work required on any game.
I feel that the best hope we've got is that devs finally let go of multiplayer and then maybe, just maybe, we can get a proper indie RTS. I have no hope whatsoever that large devs will ever try anything without multiplayer, and that means multiplayer will either be the focus to begin with, dooming the game to fail due to having to compete against SC2 or it will be added despite being pointless, taking resources away from the main game (see Spellforce 3, a good game, but could've been better if they spent no resources on a multiplayer nobody was ever going to play).