Thrawn was a great villain, I agree, but we've already had stories about him. I'm not so sure that he should reappear in JKII.
For me, part of the attraction of the Dark Forces series has been following the story of a new central character (Kyle), and tackling new threats to the universe. through him. You didn't really know which wat the story was going in JK, because it was original, with original characters.
With Thrawn we already have preconceptions. We know that he is a master strategist, a plotter, a tactician, and an art lover. We know some of what makes Thrawn tick, and therefore some of the unpredictability of the story is lost. For example, if you entered a chamber that contained Thrawn, the first thing you would probably do as a Force user is look for Ysalimiri...or Noghri.
With completely new characters, you should have no preconceptions, and have no idea of the feats of which they are capable. That forms part of the enjoyment for me.
This is why I sometimes get a little tired of the EU, because the writers keep returning to the core characters seen in the films. Although it is interesting to see how they develop over time, sometimes it feels more like immersing yourself in a TV soap (a genre I do not enjoy).
By the same token, I think mistakes have been made in the EU by introducing some totally radical concepts which would probably be more suited to Star Trek, and a quest for even bigger and badder weapons than the Death Star, some of which seemed out of place.
Sometimes it is useful to return to basics, and just tell a human story. A story about the struggle of the few against the might of the many, and the sacrifices they must make to succeed. Although such a story could be told in the context of a Thrawn scenario, there is still the problem that Thrawn is not a new character, and that we would have preconceptions about that character.
A new villain, with new tactics, new powers, new allies, would be fundamentally more interesting due to all of the unknown factors, IMHO.
The only true constant in the Dark Forces saga should be Kyle Katarn, because the series tells his individual story. I would even have to say that Jan could be expendable - although, in another way, I've come to think of her in a similar way to Wedge Antilles. A survivor. Someone who faces trials by fire, yet somehow, somehow manages to come through those trials.
Just a thought.