I just finished reading Thrawn Treason. Best of the 3, imho. The books started the wheels turning a bit. The Thrawn from Rebels doesn't seem to be as competent as in the books. I recently found out that Dave Filoni and Timothy Zahn have said that both Thrawn and Ezra survived the Purrgil taking them into hyperspace. So the next part will contain parts from the books, which if you haven't read, would be contain spoilers for them.
We all know Thrawn is intelligent and can figure out battle strategy from art work. In Thrawn Alliance he was able to deduce that Vader was Anakin. Though Vader denied it and told Thrawn to never speak of the Jedi again. Thrawn also figured out about project stardust with the help of Eli Vanto by following the supply lines. In Thrawn Treason, he discovers that a fellow grand admiral is guilty of treason, laying out an entire battle plan for Commodore Faro to follow to defeat Grand Admiral Savit, in spite of being at a 3 to 1 star destroyer disadvantage.
My next point has to do with second and third sight, which the Chiss use those gifted with it to navigate through hyperspace. Basically, these young girls have a force sensitivity. It is a guarded secret among the Ascendancy.
My theory as to why Thrawn is not as formidable of a foe to Phoenix squadron is that it was designed that way by Thrawn. I doubt that Thrawn would forget to do his research and discover all the secrets that could be learned before engaging Ezra or Kanan. I would like to believe that Thrawn dug into the history of the Jedi and order 66 and was able to figure out what happened and who Palpatine truly was. The final chapter of Treason has Palpatine ordering Thrawn back to Coruscant to question him about possibly being a traitor himself. Being executed didn't help the Chiss fight the Grysk, and for other obvious reasons, Thrawn didn't want to die. Since a tactic used by Savit in Treason was to make freighters for stardust disappear with jumps to hyperspace and blame the accidents on grallocs, I think that Thrawn was setting up to leave the service of the Emperor, due to Palpatines order. I think that Thrawn was able to convince Ezra to pilot the Chimera through hyperspace, just like a Chiss navigator (also Vader did it too in Alliances) and the two of them disappeared into the unknown regions. Thrawn did send Eli Vanto and Assistant Director Ronan to the Ascendancy. I think Thrawn would see the usefulness in having a Jedi to fight the Grysk and would attempt to utilize Ezra for this purpose.
Just my theory on why Thrawn wasn't as formidable in Rebels as he usually is in the books. I haven't really refined the details a lot, but it is one possibility.