I honestly don't remember what I thought about when Obi-wan said "the clone wars": but it definitely wasn't actual clones...
I'm actually a huge fan of Plinkett's suggestion about the clones and how the war should take a toll on Coruscant itself - there should be a draft for the Republic army (go on to be the storm troopers, no clones), war torn buildings, poverty, etc. That would make the war feel that much more real.
One suggestion I have for AOTC, remove Zam completely and that assassination attempt. It goes nowhere honestly. You can have the kybar dart be a piece of shrapnel found on the landing platform from the introductory assassination attempt. Obi-wan then gets it analyzed and the droids say it's from the Kamino system or whatever you want them to say.
So the first act of AOTC would be this basic flow:
-landing assassination attempt
-Padme addresses the Senate deleted scene (explains very clearly WHY she is targeted for assassination)
-Chancellor's quarters about Padme needing extra protection
-Jedi Council giving Obi and Anakin orders to investigate and protect Padme
-Obi investigates kybar dart deleted scene
-Padme and Anakin leave for Naboo
-*newly created scene* as Anakin and Padme fly off above Coruscant (he's piloting a small ship just for the 2 of them), Slave I surprises them and there's a bit of fancy manuevering for Anakin to show off his skills a bit, and Anakin and Padme blast into hyperspace just in time
I also like the idea of Anakin being just another Jedi in training. No chosen one prophecy or anything. Anakin and Padme know of each other simply because of Obi-wan and Padme being connected in the past - don't need anymore up front explanation other than that. (edit dialogue around this - no surprise at how much Anakin has grown, he hasn't seen her in 10 years, etc) Romance blossoms while he's protecting her.