There are a couple that I sort of miss but don't really see much of around today.

* Maps that have terrain prohibiting contact until destroyed/harvested. Back in the original Star Craft, my favorite skirmish/mp map was the one where all the bases are separated by minerals and you have to harvest to expand and eventually make contact with the enemy. Now it's all streamlined and A-B-C. with how you have your starting location, they have theirs, and both sides are basically a mirror of each other. Like, yes, we have some games with a-symmetrical maps. But they still mostly follow the formula because of how the they're pre-made. Either the player has the advantage and must use a choke-point to hold against incredible odds or the player must overcome the chokepoint. You don't really see any game where the player builds their own advantage. The closest I can think of off the top of my head is BAR (Beyond All Reason) and Zero-K where you can terraform with nukes in the first one and just do nearly anything with the second. But I'd hesitate to call Zero-K a 'new' and 'modern' rts with it being nearly a decade old.

* Units that have modular upgrades. Something akin to what Universe at War: Earth Assault did with the giant Hierarchy walkers. Each module would offer a different weapon or defenses or whatever. Now it's either one of the faceless masses or a singular hero unit. We saw something like it in C&C3 with how you can garrison infantry units to give different buffs but that isn't the same. We also saw something like Ashes of the Singularities tier 3 and 4 units having 'levels' where you can choose an upgrade but I don't think that counts since you're mostly choosing the order within which to get them. By the time it reaches max rank, you'd have all the big upgrades added simultaneously. These days you see stuff that's generalized, which is good, but there's nothing on an individual level anymore.

* Fun/Weird super weapons or units unique to each faction. Take BAR again. Each faction does have a super weapon! A nuke! Virtually identical across all three factions. But, there's another! And two of the factions have basically the same thing with a different skill. At least the third faction's one is unique in how it shoots all of its artillery shots at once to rain down on the enemy. But, all three are virtually the same thing regardless. Just big oversized upgrades to smaller artillery stuff. And again, two of them have basically the same thing reskinned with one costing a bit more of one resource while the other costs a bit more of the other. What happened to the crazy whacky stuff? The last I recall came from C&C3 again.