Shadow Hearts 1, 2, and 3. For Vita.
I could not agree more with this. I LITERALLY just started playing the first one over again two nights ago since I got the first 2 games for my birthday. (I've played through all of them but sold them when I was younger when I used to sell my games when I was done with them. I wish I could slap my younger self)
Even for a game that's 11 years old, it still has some great writing and characters. :)
A Legend of Dragoon remake would be amazing, as would a Wild Arms 2 remake. But those have been mentioned.
If I had to pick one of my all time favorite games that would be amazing to see redone, it would be Suikoden 2. I don't need to see it in super 3D graphics. Just update it a little with higher quality sprites or even go the way of Suikoden 5. 3D, but still colorful and anime-like. All that, along with some anime cut scenes and I would pay any amount of money to have it in my hand. :)