My suspected Disadvantages:
1) Need a bigger case that will allow mounting of 2 supplies (Duh).
2) Need to wire up a/the power switch for the second supply (atx).
2b) Need them to both turn on at the same time... or else you may have sync problems starting the system board with one supply and the accessories w/ the other.
3) You may not be getting the power to where it's needed...
EX: There are 3.3v 5v and 12v lines in a power supply. If all your motherboard items are using the 3.3v power and the supply isn't enough to satsify that need then adding a second supply isn't going to help because you won't be providing power to the motherboard, just to your peripherals. (Of course, if any of you perphs are using 3.3v and you move them to the new supply that leaves more power available to the motherboard items... but... now you are managing the power).
4) You have the potential for ground loops having a motherboard powered off of one supply and accessories on another. I don't think this would cause problems, but, it is a remote possibility.
5) For the extra $20-25 you paid for the 250w supply you could have spent extra to get a case w/ a 300w supply and not had to deal w/ any of this.
In summary, basically no huge disadvantages that I can see, but, kind of a pain in the a-double-s to manage.