The CD-ROM hasn't been any annoyance to me so far, there's about 40mm of space btwn it and the PSU. A few problems I have with the Aria are:
1.)The PCI bracket - There's a total of 6 screws, 4 for each slot and 2 for the bracket itself. Any time you wanna remove an expansion card every screw needs to come out. It's annoying as all hell if you dismantle your rig often.
2.)The PSU has 8 screws holding it in, along with a support bracket. A lot of people recommend removing the PSU and support bracket when installing the motherboard and heatsink, so I did, and it was a PITA. It's not necessary and I don't recommend it, I can slide the mobo and heatsink in without removing the PSU.
3.)Cable management is a nightmare, the length of the cables are ridiculous. I guess it's necessary to accomodate all types of mobo arrangements, but they overdid it a little. I'm not even using the card reader or any of the front panel USB/Firewire/Audio ports and it's still pretty cluttered in there.
4.)Not really a problem with the Aria itself, but MATX boards in general. My video card's PCB extends out right next to the ram slots and blocks the locking mechanism. So any time I need to pull/install a ram stick the video card needs to be pulled up some, which means all the screws for the PCI bracket have to come out again. The drive cage usually has to be pulled for just about anything as well, but it's not too bad, it's plugging the perhiperals back in that's the worst part. I've gotten to the point where I can do it by feel without looking.
There's no accomodation for a floppy drive, I have an external USB floppy that I use. If you've got XP SP1 or higher you won't need one, otherwise I'd just leave a side panel off and run a floppy cable to the drive outside of the case. Actually I'm not even sure if there's a power connector for floppy drives, I don't recall seeing one...you may need an adapter for that.
As far as a s939 boards, I'm not sure if those will be out anytime soon. There may be some already, just not mainstream and readily available. MATX is a pretty overlooked form factor. I've talked with a Foxconn rep and he told me to expect overclocking boards (so far there are virtually none) in 05, so they've probably got a few things in the works.