Well, there doesn't seem to be any interest in a warcraft RTS as they are progressing the storyline in the mmo, but I wouldn't mind seeing them make an rts based in draenor pre-portal or perhaps the war of the ancients...
There's actually a lot of stretches in the timeline that would have a great story, multiple recognizable factions, and could use a little in-game representation outside of the novels.
Otherwise, I'm having some trouble thinking of any for some reason... I've forgotten their names but I always thought it might be cool to see the younger Auron, Jact and such from FFX. Sticking with final fantasy, I think a direct prequel to Final Fantasy tactics covering that War of the Lions that (if I recall correctly) lasted some 50 years and Ramza's father would be cool.
I always thought it would be fun to play during the era of Tiber Septim in Elder Scrolls, either helping him to establish the empire or assisting the various different native races in resisting, but I suspect the sheer scope of that game is simply too large to ever be a reality. Strangely, all of the major games have taken place rather late within its own timeline (all post-third era), a bit like warcraft in that regard, so there's plenty to explore.