Hostile Waters: Antaeus Rising. Been ages since I last played it, but I remember it was pretty sweet.
Also, Battlezone. this one lets you control one of your units, and give your classic RTS orders.
Disclaimer: I have not played the remake, and I don't remember whether Battlezone 98 is better or worse than Battlezone 2.
BZ 2 feels more like a traditional RTS where you can hop in a hovertank to show the other pilots how it's done.
BZ2: commanding from the front:
You also have Carrier Command, which is even further apart from your traditional RTS:
You get a carrier (I know...) that can produce aircrafts of tanks.
And you can pilot any of these.
The unit count is low. The AI feels like it was made to emulate a drunken baby pilot, but there is no other game like that.
The unit cap is very low (4 aircrafts and 4 tanks), but you can take over sectors to get better weapons to mount on your units.
It is still no traditional RTS at all, and not a very good game (mostly because the AI is completely unable to stay grouped, which forces you to do a lot of babysitting), but mods did somewhat fix it, and it was rather cool.