@matt.
I use the NUC i5 version as well for my media center. It works very well. I have windows 7 256gb SSD, and Bluetooth and wifi built in card. I use the PS3 remote as its Bluetooth, the range is very good. Very detailed and far range. I also use the Bluetooth Lenovo keyboard with trackpad, but I do see myself using the Logitech wireless keyboard a lot more as its very stable.
I had played around with FLIRC for Infrared but that wasn’t close to being as good as the Bluetooth version. The PS3 remote is very stable and a very good build quality. Can’t go wrong with Sony. If you need help with the mappings, let me know anytime.
The cable is slightly large but you can squeeze it in if you like. However a big point to note, the Internal IR or FLIRC both wont work once the lid is closed. I got the FLIRC as it is known to have the best IR range.
If I were you I would ditch the IR concept over the Bluetooth solution. The remote is about 16 on Amazon. With that price range you can’t go wrong. Besides you will have to buy the internal Bluetooth card. Below are the links for the remote and the Wifi/Bluetooth component.
Bluetooth + Wifi. Note: I use the Bluetooth from the combo only.
http://www.amazon.com/gp/product/B009SJTSWU/ref=wms_ohs_product?ie=UTF8&psc=1
PS3 Remote
http://www.amazon.com/gp/product/B0050SX9I2/ref=wms_ohs_product?ie=UTF8&psc=1
Another thing to note is that if you do decide to go with the Bluetooth version, I suggest stick to the recommended card I’ve mentioned above. There are a lot of after market cards which don’t function very well. The one mentioned can wake up with no delay from a hibernated stage of the remote.
Also if you want to wake up your nuc from a sleeping state, Windows 7 and Windows 8 function differently. Windows 7 can wake up from a shutdown state where as Windows 8 can only wake up from a hibernated state. I’m not sure if that has changed. I wake up the nuc with Wake On Lan on windows 7. I use a software called hipporemote on iOS which has a power button. Shutdown is never a problem.