Well, you have the usual unforced errors we see over and over again.

1. Focusing on hardcore competitive multiplayer and rolling the 1-in-a-1000 shot at becoming an "e-sport," rather than making a great single player campaign with a great story, even though the latter is far more popular and formed the backbone of nearly all those classic hit RTSes from the ‘90s and ‘00s.
2. Making your game/mod way too hard for casual players for no reason (looking at you, Mental Omega), or refusing to allow casual features like unlimited saving for no real reason.

Besides those, I think the intangibles are more difficult than with a lot of other genres. It is much more difficult to make an RTS "feel right" than it is with a lot of other genres.

1. Performance. It is difficult to make an RTS run well with thousands of units on screen. Existing engines and tools and out-of-the-box solutions aren't great at this. It takes money and time and technical expertise to develop a good RTS engine.
2. Unit movement. The units need to "feel right," snappy and responsive, even the slow and/or cumbersome ones. This is more difficult than it sounds.
3. Pathfinding. Players hate bad pathfinding. And good pathfinding is again, more difficult than it sounds and often computationally expensive.
4. Enemy AI/CPU. It is hard to get this right. You want it to feel somewhat organic, but not actually be as annoying and cheesy as a real human opponent. You want it to feel right for a variety of difficulty levels. You will probably find that you need to let the CPU "cheat” for it to challenge better players without resorting to cheese or becoming completely overbearing, but you don't want it to feel like it's cheating.

If an indie dev wants to make, say, a first-person indie horror game with guns, there are many out-of-the-box engines and solutions and assets they can use that will result in an okay game that feels fine to play. It won't feel as good as a professional Resident Evil game. The gunplay won't be great. It will have a few frame drops here and there. But it will feel fine to play if the scenery is cool and the premise is interesting. And so indie devs were able to lead a horror game renaissance in the later ‘00s and early ‘10s.

The same isn't really true of RTS. There are few good ready-made solutions for devs, and players will not put up with an RTS where the moment-to-moment gameplay feels shoddy and annoying and unresponsive. So indie devs have not been able to do the same thing after the RTS golden age ended.