hey, I just found in the net a spoiler for the saga main capaign
it may dosen't say about missons, and characters, but it gives you nice idea about how the general storyline will go, and it corresponds nicely with the teaser trailer (the one starting with blackmane style base explosion. of course i won't say here where you can find it - you must search for yourselves:D
Fom what is written there it would be easy to make a crossover with WC3 characters. if you still don't want to do this, well... IMO it's a good decision. the problem for you guys will be finding voice actors to replace WC3 ones. it's not about you having bad voice actors (from what is heard in the teaser mentioned above they're great espetially the british-accent-guy, the one that says "I'm picking three Kilrathi carriers at extreme edge of our sensors" i hope He is still in the team), but anone who played jedi knight 2 or jedi academy will know what it means to replace Mark Hammil with some other guy, and lucas arts coud use much more resources than you can to find the best replacment.
Anyway the story looks really great, keep up to this