my idea would be to make it something like ghost recon.
by that I don't mean a first person shooter, but with a comparable set-up, ie: you pick from a list of missions/chapters and each completed mission opens up the next in chronological order. after you pick the mission/chapter, you select who you'd want in your party to try the mission with.
chapters could be grouped in campaigns, eg a holt or sun village or quest campaign. what you do in a chronologically earlier mission should affect later missions: you could, in a way, go back in time to correct things you think went wrong, or try them with different characters. depending on how you play the mission you could open up different chapters or mission paths or even different campaigns, kind of like old choose-your-own-adventure gamebooks. btw, i don't mean campaign in the wargame sense: i just mean a set of chapters that follow after each other.
you could use cell-shaded graphics. i think they could be made to resemble wendy's art far better than regular 3d-graphics and they would make for a great and seamless transition between cut-scenes and gameplay. correct me if im wrong, but they are also far less demanding, freeing up possibilities for larger levels and more dialogue