A "Puppetmaster" is supposed to "pull the strings," so to speak, of their puppet.
I know it sucks that the other pet jobs get some cool stuff but part of the game/skill with PUP is that you're not supposed to choose spells or weapon skills, but instead work with the puppet and pull it in the right direction. It separates good from bad Puppetmasters at times, like the impatience with overloading.
This is as SE intended it to be and I really hope they don't change this system just to make it "easier for the players."
The AI is supposed to be somewhat of a struggle... until you get to know it. Not saying the system is perfect, there's a few bumps in the road like that whole -na spell situation.
Now for the Ashu Talif questline... people like to complain about this because it's difficult and a bit out of the way, but it's totally doable. It's even easier now with the level cap increase, and all in all it's a ridiculously fun series of BCNM's. Yes, it is extremely hard to put together, but the reward is completely worth it.
Also, I'm just as lost on this Tactical Processor issue. I'm sure SE knows we're still writhing in pain about it.