I think this has fantastic potential because it would encourage the porting of commercial applications. The flip side is, as stated, that it discourages free apps to a degree. I think overall though, it would ease the feeling by many commercial developers that Linux users will be unwilling to pay for any software. I am thinking here particularly about games. Making paid apps easier to get are more easily supported, a la andrid market, would be a boon to the viability of creating linux apps for companies.
I agree that I would want to keep synaptic and gdebi for ease, speed and tweaking but this also depends on how they plan to design the app store (am too lazy to try out the first build).
The other obvious disadvantage to the above positive would be the specificity of this to ubuntu, again limiting its potential to promote commercial application development.