Lots and lots of coolness in that episode...
First, the Zilla Beast being an homage to Godzilla and King Kong is great. You can see the more Kong-laden episode in next week's, but there were definate overtones in this one.
I liked the nod to a "superweapon" bringing about Zillo's existance too... It was hardly an atomic blast, but it was big and did some awakening.
Also the "Dugs are pricks" message was interesting I thought... They're careless with their own planet, like to blame others, and just sorta seemed like sneaky jagoffs at the end of the day, that hated something tha twas just trying to survive. Again it's a Zilla-ish overtone there (those who liked him and those who wanted to destroy him struggling against one another).
Then putting him to sleep? Classic Kong stuff.
I caught the weird nod to MASH too... Why? Hmmm. It's neat, but there didn't seem to be a reason for it, plus one's dead anyway.
I really liked the way the episode opened up too... That's combat in the Clone Wars more as I imagined it. Big battles, insanely overwhelming Separatist forces facing Clones that are outgunned but are better fighters. That more represented what we saw in Episode 2 than I think many episodes have shown. The movie was more like this, as was the Geonosis Story Arc. I liked seeing a really massive generic Sep army though, ready to do real battle over an important planet for its resources.
It's like Germany wanting to divert their attack on Russia to capture the oil fields in the South, or the entire conflict in N. Africa in an effort to capture and control mid-east oil fields in WW2. The fight over resources to simply keep fighting.
This was one of my more favored episodes of Season 2 so far... Right behind Landing at Point Rain. It helps that I grew up loving classic horror monsters like Godzilla and King Kong too, haha.