I'd say go for a Silverstone FT03 for the case - works excellently with the Gene-Z mATX board and will fit all your components in a far smaller footprint. The only change needed would be to switch out for a slimline optical drive.
That's a possibility in the future, definitely, but long term, not the short to mid term. I mean more about space than anything else, which is why a larger case appeals to me. That being said, Ljs makes an excellent point about putting a m-ATX motherboard in an ATX case. I may well go back to the Fractal Design R3 as you suggested to be honest - it is an awesome case and, if I decide to go watercooling in the future, then I can look at getting a more appropriate case at that time.
If I had to do it all again and a nice budget like that, I would go with something like this: Think that is everything, apart from HD which is a bugger atm.