1. hard to see potential cracking/damage to the carboy... it would really suck to load one up with 5 gallons of beer, only to have the weight cause it to give way when you go to pick it up, and have it all come crashing down, and potentialy injure you in the process.
2. hard to see what is going on with your beer... with a bucket, they are not only translucent, but you can also take of a very large lid to see inside. with a carboy, you have a very small neck, and if you don't paint it up all the way, then you will still have to put a t-shirt or something over it anyway, to block out the light from the top area that was unpainted so that you could see what was going on inside your carboy.
3. much harder to ensure that you got it clean, since you can't easily see down inside of there, since you don't have a nice wide open area like in a bucket. To me, this would be one of the biggest reasons not to do this.
As the mantra goes
Sanitation... Sanitation... Sanitation...