-Golden Sun + Civilization (As 'the nature of civilization' is a heavy theme in the series, this would be good - build/rebuild Weyard, factor in alchemy, factor in the Ancients and the lighthouses, etc.)
-Halo + Homeworld (Considering how many ship classes exist in Halo fiction, and how there's a strong groundwork for how ship battles function in the setting, plus the glimpses of it in Reach, I think there'd be great potential for a ship-based game)
-Heroes of the Storm/League of Legends + Warcraft III: The Frozen Throne (A singleplayer MOBA mode to explore the setting in the same vein as The Founding of Durotar)
-Killzone + StarCraft: Ghost (Well, we're never going to get Ghost anyway, so either let us play as a shadow marshal or Echo, considering that in the current state of the fiction, the UCN and helghast are in a state of cold war anyway)
-The Legend of Zelda + Final Fantasy (As in, a traditional, turn-based RPG where we get to explore Hyrule as not the Hero of Time, but a band of other adventurers. Or have Link as the warrior, Zelda as the cleric, and, well, use your imagination)
-StarCraft + Mass Effect (StarCraft space RPG in the Mass Effect style)
-Mortal Kombat + some WRPG (As in, the chance to explore all the realms, and actually delve into the fiction. Keep the gore too if you want)
-Star Fox + Wing Commander (Give us customization over our ships, allow us to explore the Great Fox, give us a story that doesn't abandon the 'essence' of the setting, but is beyond "Andross attacks! Again!)
-Warcraft + Dragon Age (Singleplayer RPG that allows us to explore Azeroth)
Edit: Will also nominate:
Command & Conquer (Tiberium setting) + Fallout 3 (Wasteland RPG set in a world that's being consumed by tiberium)