The only reason (that I'm aware) of the $1000 withdrawal limit is attempted compliance with FinCEN regulations. Without the withdrawal limit, MtGox would classify as a money transmitting business (instead of a provider of stored value) and be subject to many more financial regulations.
Either we need somebody big to enter the game, or we need an anonymous exchange of some sort, that will not operate under financial regulation. I just don't see one of these hobbyist (I mean that in the most positive way possible) exchanges going big time and subjecting itself to the complexities of US (or other state) financial law.
Why is it that mtgox has to abide by the rules of FinCEN which is a US institution! MT Gox is owned and operated in Japan from what I know, so once again what is it with this deference toward US financial authorities - you know not everything has to revolve around the US
I for one would prefer no withdrawal or deposit limit BUT in exchange I'd be willing to accept the implementation of KYC rules (know your customer) That's a small price to pay for increased transaction freedom. This way authorities feel safer that bitcoins are not being laundred for shady purposes via these large exchanges (if they wanted to launder it they should do it person to person ie direct payments).