Beyond All Reason is AMAZING. I can't say enough about it. Its my favourite game, and totally annihilates (!) the competition.

Though I guess the competition is pretty small for large scale RTS. Maybe:

• Total Annihilation
• Supreme Commander
• Ashes of the Singularity
• Sins of the Solar Empire (sorta)

BAR has fixed all the UI/UX problem, scales well, has a big community, is free, fun, and super deep and complex.