i think I'm done with FCP...although a nice little program, it seems that it is far more important to apple to create a huge piece of crap (iPad) than to actually spend time and polish professional applications.
A nice little program?
It's your media drive. An eSATA to USB will send data at USB speeds, and is not a good practice.
This isn't a FCP problem in my view; it's a workflow and hardware problem. It doesn't have anything do with the iPad.
I don't believe that AE is going play well with raw footage or play it all.
My suggestion is to get a fast FW800 drive and transcode to AIC or pro res, and get into intra frame as quickly as possible especially if you intend to use AE.
Because AE isn't build to handle native mts.