I'm pretty sure the difference is huge...
I have both. In real world performance without anything crazy, it's not a huge difference between HD 4000 and Iris graphics in a mobile processor. They are integrated graphics and remain a bottleneck, but said bottleneck isn't as bad as it was say five generations ago. Civ 5, I use the same exact low settings I use on my HD 4000 MacMini, and the fans kick in right at the same time on my Iris rMBP 13". I get maybe +2-5 FPS increase on my Iris if I'm lucky. You aren't going to get magnificent 3D rendering times either, so I guess you're thinking of Iris PRO available on the 21" iMac & base rMBP 15" right now.
Iris graphics isn't enough to kickstart sales of the MacMini. It's 2013 tech, and the MacMini should've already had it last year. Apple has to do more if it wants the MacMini to bring in proportional gross margins and sales to the iMac line. Since they don't sell a whole hell of a lot of them, they either need to figure out how to sell more units with attractive tech and value that makes a good chunk of their target market jump out of their seats to buy it, or EOL it. It can go either way at this point.
I stand by my prediction we won't see a new MacMini until 2015, and this is all at the feet of Intel.