I think my least favorite thing about the Post-ROTJ novels is how pacifist and do-nothing all the Jedi are. Obviously this decision was made way before the Prequels came out and now they're stuck with it. But the Prequels showed the Jedi to be war generals while the NJO Jedi had a long tiresome debate about whether they should be fighting an extragalactic invasion because it might turn them to the dark side
Much as I love Luke in the Post-ROTJ novels, his reluctance to take action is really annoying.
To be honest that's the debate I wish they had had in the Clone Wars. Perhaps not onscreen but in a novel or comic, or it could have been more of a long-running theme running throughout the PT. I think it popped up every now and then, but I think the Jedi took to being generals a bit too fast. I mean, there seemed to be that at least some planets had militaries, and many of the ships were staffed by clones and other officers, so it stands to reason that there were trained military officers out there. I think there should've been some debate at least about if the Jedi were the best choice to be military commanders when there were other trained officers out there. It would seem like the Jedi would be mediating the war, not leading it, from how they were described in TPM.
Granted the comics which predated it showed all manner of Jedi warriors, but the movies supercede them in terms of canon. If they had bought the Jedi in as generals after the failure of Republic forces, or maybe the CW had led to a schism among the Jedi, with some fighting, some abstaining, similar to how things went down in the Knights of the Old Republic comic, I think that would've made more sense to me.
I never quite bought the Jedi jumping forward to lead this army created for mysterious purposes, which was just conveniently produced in time to counter the Separatists. It seemed like some Jedi at least would be suspicious of that.
As for Luke's reluctance, to some extent I disagree. Luke has taken the field in every major book series I've read. Now, the problem is that they've made him so powerful that the battles might become lopsided or they have to make the threat so powerful that it's ridiculous. Or they have to make up some excuse to have Luke hold back or to avoid fighting, or going all out, like he's afraid of going to the dark side or something. The desire to make Luke the greatest Jedi (notwithstanding the PT making Anakin the 'most powerful Jedi ever'), has limited them a little regarding story. Though I think Del Ray has done a good job producing some villains like the Yuuzhan Vong and situations that at least test or strain Luke's abilities sometimes. They present obstacles that couldn't always be solved with a simple lightsaber stroke. Some of their villains, unfortunately, like in LOTF, never live up to the hype, but NJO and FOTJ offered some pretty worthy adversaries.