I've been thinking alot about the same, and there are different things to keep in mind when you argue GPU vs FPGA.
The pros of GPU mining is - Resale value. The GPU market is always there, and GPUs can be used for lots of things besides mining
- Lower entry price. The $/mhash is significantly lower on a GPU than with a FPGA. The BFL single is closing this gap somewhat though.
- Hardware flexibility. Find a old computer at a recycling center, change the PSU and you can use it for mining. GPU mining needs little besides a good GPU!
The cons - Heat. GPUs produce alot of heat
- Noise. Constant tornadoes in your room. I haven't slept properly since about March 2011
- Electricity. GPU mining uses alot of juice! Living in countries where the $/KW price is high can effectively ruin mining
- Space. GPU mining takes up alot of space, especially when you start your multirig 9001 Ghash/s rigs.
The pros of FPGA mining - Less heat than GPU mining
- Less noise than GPU mining
- Uses considerably less electricity than GPU mining
- Takes up less space than GPU mining
- No tornadoes
The cons - Higher $/mhash price
- Resalve value. Now i'm not entirely sure about this one, but to my knowledge FPGAs can be used for passwordcracking or renderingfarms, and probably other things that i haven't even heard of. I'm not sure how effective specialized BTC FPGAs will be at either of these, but i'm sure they can be tweaked to work for these purposes. Renderingfarms are needed/used at schools and other places, passwordcracking is abit more shady.
These are the only things i can think off. I'm sure someone out there has more to add to this list, or something that is wrong with that list. This is just what i've picked up in the FPGA/GPU debate. I myself will be GPU mining for aslong as i can. I currently pay nothing for electricity, and if i have to one day in the future, the Kw price here is $0.06, so nothing major. If i had $30k and had the patience to wait 15 weeks for the BFL rigbox i would probably invest in one. But that's a different story
Hope this helped answer atleast some of your questions!