Thrawn has the grasp of unusual tatics and is the less conventional of the two. Palleon has the better record and a much nicer relationship with his men which in turn means they have a much better flow. But Palleon would be my choice due to his lifetime's worth of experience and good tatics backed up with the one shot affairs Thrawn favored.
It is stated in The Last Command that the men under Thrawns command would die for him, which I would say equates to a pretty strong bond between him and the men under his command.
I don't think you can really put Thrawn down for being a bit fanwanky in his strategic genius, considering most of the major SW characters are a good deal worse. Why can't there be one person in however many trillion inhabit the galaxy, who has an incredibly rare skill in strategy and tactics? Luke Skywalker seems to be invulnerable to death of any kind, be it thousands of stormtroopers, vacuum, explosions etc, but its ok, cos he's a jedi...
Thrawn is my favourite SW character, with Pellaeon or Wedge coming second. As for Pellaeon ordering the retreat, and not receiving a court martial, perhaps it was lost amongst the chaos after Endor, along with the counterattack which logically should have happened when the Rebel fleet decided to just sit in Endor orbit, or at the very least the slagging of Endor. I know I wouldn't have hesitated to BDZ Endor, I'm sure an Imperial commander wouldn't.
I have no doubt that if two factors had been prevented, the Empire would have been taken to victory by Thrawn. Firstly, Leia gets shot or somehow else killed on Honhger, stopping the Noghri rebellion. Secondly, Thrawn sends the spec ops team to Coruscant, not with orders to capture the Solo twins, but just to nuke the place, meanwhile spacing C'Boath, he'd reached the end of his useful life anyway.
This means no more rebel leadership, no Wayland strike force, no Rukh backstabbing, and surely eventual victory. The Reborn Emperor would have returned, but then died due to the faults in his cloned bodies, leaving Thrawn in overall command, then just crush or incorporate the warlords, and prepare for the Yuuzhan Vong invasion, which Thrawn may or may not know about from his time in the Unknown regions. Either way, under these conditions I'm sure the Vong would be more easily defeated.