Turn Xcom into an FPS, and make SMAC a Sims style game where you create your own Mind Worm, get a job, and spawn some children in the planetary fungus.

Wait a second, I think some sick twisted part of me might actually like to see that last one.

But in all seriousness, I'd make some changes to FFVI's battle system to make it actually challenging, give it an Amano style 2D facelift and end the changes right there.