I've read every single book put out in the star wars mantle, including the mandalorian armor trilogy and the lame ass lando calrissian trilogy.
the way the clone wars are supposed to work: (already been mapped out many years ago)
the clones are the republics answer to the trade federation's army in the movies. in the books there's no trade federation and the republic didnt use the clones. they fought the cloners and were losing until the cloners attempted to accelerate the growth process. this left the clones unstable. (turns out it's because the presence of the force, since such accelerated growth is unnatural. Grand Admiral Thrawn solved this with ysalimiri)
i hope he doesnt radically change this, becaus it puts all of the books in a bad spot.
why is palpatine doing what he's doing with padme etc.?
well assuming you have already figured out that palpatine is the future emporer, everything he's doing is to eliminate the jedi council, the senate and build an army and a base of power for himself. it's still unknown who palpatine's master is, i speculate Exar Kun in some form, but i dunno.
he wants amidala killed because she leads the loyalist party - the party OPPOSED to the creation of any army. the first attempt just killed her decoy, the second attempt was thwarted. so he played the jedi against themselves when they ordered her to return to naboo, and played jar jar binks to forward the motion that she herself would never give.
there are a lot of loopholes that are being filled with SHITTY writing. i went and saw it for the third time today and after seeing how empty the theater was compared to how sold out spider man was i can only hope he'll ask stackpole/anderson/zahn/salvatore to help with the script a bit. wishful thinking after seeing his interviews.
then again he clearly has no love for the books he's already approved. in the phantom menace during the scene when amidala's bodyguard enters and says that palpatine has been nominated to succeed chancellor velorem, he says 'bale antilles of alderaan' as another candidate.
1) antilles is a corellian name, wedge's surname. he was not born yet, but his parents owned a refueling station during this time.
2) bale's last name was organa.

this may seem nerdy, but the star wars books are really really good even if taken apart from the movies. the best ones in my opinion are:
the ENTIRE X-Wing series, all 9 books are consistent and amazing.
I, Jedi by Michael Stackpole
anything by michael stackpole
the hand of thrawn duology
the entire new jedi order series
the black fleet crisis
rambling. i have high hopes for the third movie, since anakin becomes darth at this rate. it was my understanding that he was married and had kids before finally falling. i guess we'll see if lucas follows what was already laid down.
waelos - those bugs are geonosians and they dont turn up later. neither to troydarians (watto) nor a lot of the aliens seen here. the empire is a racist regime akin to nazi germany, and palpatine was known to wipe out entire races or use them for experimentation.