Aside from the Thunderbolt
Aside from the Thunderbolt and the Core i5 CPU, an Early 09 iMac is going to have pretty much the same array of connections. Even more, in that it will probably have a FW400 port instead of just FW800. And while you'd likely have to pay the $30 for it, there's no reason the iMac couldn't run Lion.
Gigabit ethernet has been a staple on all Macs since around the switch to Intel CPUs, and the iMacs have had FW800 connections for quite some time now as well. Video rendering is far more CPU intensive than RAM intensive, so even if the RAM were slightly better in a Mini it wouldn't do much in the way of speeding up the rendering process.
So most of your proposed benefits aren't unique to the Mini or aren't that beneficial. I will definitely grant that a Core i5 is a better CPU than a Core 2 Duo, but neither system is designed for even light video editing work. Any time the CPUs start getting up around full utilization for more than a few seconds, you're starting to overwhelm the cooling systems. The iMac has three fans, and each one of them is about 2.5-3X the size of the single fan in the Mini. The heatsink for the CPU on the iMac is also significantly bigger on the iMac, which gives the fan more time to push the heat out. We're really talking degrees of damage here, since virtually any rendering project is going to cause a lot of excess heat to build up in the unit. Heat neither unit was designed to handle. The iMac's size works in its favor, even if only just.
If it weren't for the whole licensing thing, I'd say build a hackintosh. Maybe a better solution would be to look for a program that runs on Windows and can import FCP projects. Then you have a much broader array of system designs you can choose from which would be far better suited to what the OP wants to do.
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