Sins of a Solar Empire with Wing Commander. Play the strategy game then, when you need to, jump into a ship and help with the battle directly.

Empire at War with Battlefront 2. The best of both worlds, strategy and first person shooting.

Mass Effect + Baldar's Gate II (i.e. Mass Effect played in the Baldar's Gate Style).

I'd love a crossover between the gameplay of dungeon keeper and any mmorpg. One side plays adventurers, the other the overlords that construct dungeons and lands for them to visit.

Kings Bounty and CIV IV

Jak II and Metroid Prime. I have no idea why.

My choice, which is weird.

Kohan cross Granado Espada (for the artstyle)

Would have Kohan-style gameplay with a Baroque-style art and units, along with magic.  It the game had Stardock-level AI, it would be a masterpiece.

Console pick:  (this is going to be really strange)

Virtua Fighter cross Buriki One

One of the most strategic games ever (yes, it's a fighting game, but it is very very strategic) which lacked some soul, combined with an obscure SNK franchise, which would be suitable to that style of game, yet had characters with plenty of soul.

Oh dear... this is basically the basis of all my game wants.

Empire at War Phoenix Rising mod and X-Wing

Sins and Homeworld

Supreme Commander and Company of Heroes Blitzkrieg mod

Star Wars or Star Trek and Eve Online

Command and Conquer and Mass Effect

Force Unleashed and Republic Commando

I haven't heard of Outpost 2 in a long time. And yeah, a good mix there.

Adding Battlefront 2 Extreme mod and the rest of the X-wing series to that would be the ultimate Star Wars experience!

I second that.

Rainbow Six: Raven Sheild and X-Com.

Elderscrolls/MoM

C&C:TS and GalCiv3 (Because it has cloaks and really good multiplayer)  

Ship Designer works for ground units. Each planet plays on a 100x100 tile map and does not have to be fully conquered to move on with game.