I'd say ...
1st determine what software you will be using to transcode and if multi threading is needed to process multiple files at once. For instance... if I transcode using QT, the software will take advantage of my 12 core Mac Pro and can do several files at once saving render time. On the other hand, if I queue them into Compressor or Adobe Media Encoder, the same number of files takes much longer. This is an example where a very fast single processor might have an advantage over a slower multi processor option.
2nd... as far as future proof... I see this mainly as a OS X issue and what will be support best going forward. Since the 2009 Mac Pro was recently moved to "legacy" status by Apple it may run out of official OS X support faster then the Mac Mini or iMac. It's not clear if the hack to make a 2009 (4,1) into a (5,1) machine would help if the 2009 is abandoned, so you might want to have a 2010 MP on your list instead of a 2009. Honestly, there is not much cost difference between the two if you shop carefully.
3rd... what is your budget? Knowing your max investment capability would be very good to know.
4th... how much storage space do you need and would you benefit from storage with faster data I/O?
5th... are you using the Mac to feed a video signal and if yes what resolutions would expect to need in the 5-7 year window? Would 4K be enough?
IMHO... a 2010 Mac Pro might offer the best foundation to upgrade as the landscape changes over the 5-7 year period. Then again, depending on your budget, buying a newer Mac Mini now and maybe another in 3 years might also be a solid solution.