I was always surprised that they didn't have more RTS games on the DS. Yes, Starcraft wouldn't have worked that well on the DS, but a game similar to Warcraft 3, with a focus on smaller groups and more micromanagement, probably would have done very well.
For that matter, I think the Wii might still have been a good choice for an RTS game. I've been disappointed there as well.
Starcraft 2 notwithstanding, RTS games seem to have dwindled a lot in prominence in the last several years, though, and I don't think they've ever been all that popular in Japan.