I'm also a fan of Environmental Interactions. For instance, Wind and dist clouds. Reduce visibility, slow vehicles, possibly prevent flight. Setup some sort of Dust generator up wind from an enemy base. Or an area you don't want enemies to fly through.
A catapult that flings trees perhaps, or A Ditch digger that can block off areas by water. Perhaps even tunnelling. or hiding ships in a cloud.
Perhaps a look at Age of Mythology would be interesting to you. As far as I remember there are many Wonders that work alot like you described.
Not really by working with the environment but the effects where the same.
And Stronghold had Catapults that flinged cadavers of cows, which could cause a pleague spreading or something like it.
There is also the possibility to use some kind of zones to make gameplay more interesting. E.g. Warcraft 3 -> blight , Starcraft -> creep both as zone to build/prevent building and healing. Or the poisionous tiberium fields in Command and Conquer. But most of the time fights are far to fast over to really make them count.
Other things are also possible, like the lava that is periodically flooding the level in the Starcraft 2 campaing (or was it Dawn of War?) or the solar erruption in FTL both damaging or destroying enemies as well as player units.
And of course there is the classic, height. Units that fire from a cliff would get a bonus agains the units down below.
If you're looking for a departure from the classic RTS you should look at Majesty 2, where the player isn't controling units directly. You are only setting bounties for specific tasks and the heroes/units will do them if they decided it's worth it. From the earned bounty heroes could buy weapons, armor and potions.
Each unit also had a level like in RPG's (not those silver/gold or veteran/elite labels) and you could put them into parties to increase their chance of survival.