Pro all the way. Don't know if the Pro still has an ExpressCard slot (an external PCI-Express x1 expansion slot for notebooks) since the introduction of Thunderbolt, but you certainly won't get it with Air.
Allows you to add an eSATA II, eSATAp II (Power over External Serial ATA), or possibly even an eSATA 6 Gb/s ExpressCard and hook up an external hard drive directly (or up to 5 simultaneously via an eSATA II Port Multiplier Hub), bypassing USB 2.0 and get nearly 2x the speed of USB 2.0 (with even SATA I) since TA is the native interface on most hard drives and all consumer hard drives.
Also the Pro will have a better GPU (Graphics Processor) than an Air. I'd get a current Mac Mini before I ever get an Air,
Plus the Air will screw you on the availability of other expansion ports.
Get an Air only of you are looking for a notebook alternative to an iPad.
I think you're underplaying the role of Thunderbolt as an expansion port. All MacBooks (air and pro) have it, and it obviates the need for eSata. One can use thunderbolt for all kinds of expansion when the need it, and maintain portability when it's important.