Mostly repeating a bunch here, but they deserve repeating.
Having just completed Alpha Protocol (twice in a row), I'd definitely love a sequel as well. They handled dynamic storytelling better than Heavy Rain and Mass Effect for certain; during the replay I couldn't believe the amount of scenarios they had to adapt the story for just to fit your actions. That game deserves a second run.
Dark Cloud 3 for sure. I tried replaying DC2 just a month ago, and a lot of it doesn't quite hold up anymore. But with some layers of polish and less grinding involved, a sequel could be the greatest thing ever.
I also have to second another proper Valkyria Chronicles on the PS3 (or PS4?). Going to the PSP was such a mistake; the fragmented maps and the loss of the visual style really damaged the core of the franchise.
Suikoden. The world isn't complete yet, dammit. There's still more stories to be told and true runes to discover.
Definitely another Xenosaga; or at least a retelling of the story that puts out all six episodes as originally intended. It pains me to think of how much more impossible this one is compared to the rest. Xenoblade was great, but it lacked some of the punch of its predecessors.