ok just my thoughts on this,
"ONE: Sev had to of been caught off guard, i doubt geonosians or droids could of done that"
perfectly possible but anyone can be caught off guard, including Sev. If your standing in a doorway with your back to it and someone sneaks up and then jumps out and starts shooting at you, you will be shocked, suprised and dumbfounded all at once. Remember Sev was through a door and in a turret we don't know where he encountered trouble. So it could have been any of the enemy factions faced in the game that stoped him.
"TWO: there were gun shots heard in the background over sev's comm, and since he would not off been caught off gaurd by droids, it had to off been the clone's blasters."
Ok, why wouldn't he have been caught off guard by droids? and even if he hadn't been caught off guard it would have been very easy for them to over power him. Remember hes just one trooper. Commandos are designed to be most effective as a team. He is not an Arc trooper.
"Sidious does something over the Republic comm (mind trick i'm guessing) and all the clones proceed to attack Yoda, Chewie, and the rest of the allie wookiees."
Um, its not mind trick and they only go after the jedi. Them going after the wookiees is not related to
The clones are geneticly altered to follow the orders of the people they work for (in this case the republic) since Sidious/palpatine is the grand chancellor for the republic the clones will follow his order directly.
In the comic for ROTS the order sidious gives the clones is called "order 66"
""well why wasn't delta squad affected by sidious' 'orders'?" well for one, the commandos were prolly on a different frequency, as their commander also seemed unaffected by sidious, and two, kinda like we were talking about in the thread about their voices, the members in delta squad are different from the "regular" clonetroopers, delta squad has the capability to think for themselves where as the clones have no real free will, hence them being very "weak minded", so either elta squad didn't hear/sence it, or they're just not weakminded enough"
Time to bust out the "spoiler tag"
cause I'm to lazy to break this up.
The order would have long after the events on Kashyyyk that delta squad was involved in. Remember the Yoda was talking to the delta squad at the end of the game informing them they were needed else where, well how could he be doing that if sidious gave the order for the clones to eliminate the jedi. Even if they were on a different "channel" their advisor would have said something. To the best of my understanding ALL the clones turn on the jedi so its very very unlikely that the 4 deltas would not be effected by these orders. As for clones having no free will, they have lots of free will but their geneticly altered to follow orders thus if yoda was to say jump the clone wouldn't say "how high?" he'd just jump. The arc troopers were the only clones that weren't altered in this was because they were required to do the most dangerous missions and usually were doing these missions on their own. Since I'm guessing order 66 has been pretty well drilled into their heads since day one I'm guessing that no matter how "Unaltered" they may be they all are effected by it.