I kinda like the size of the Courthouse, at least where I've arranged it in my town (near the police station and post office, which are dwarfed by it). I agree that the Fudge Factory should be bigger, though, and I wouldn't mind a slightly bigger Bad Dream House.
The most awkwardly sized building in the game has to be the Helter Shelter. It needs to be reverted, ASAP. I would say #2 is the mall, but I think the reason it's so odd looking is because it's not really a mall, but more of a mall entrance. It's almost like they intended for us to try to join it with other buildings or build something 3D out of it.
I agree with the pet store being too tall / awkward. The singing sirloin is another one that ought to be shrunk -- it's just not to the same scale as most other buildings.
Others that ought to be bigger: Krustylu, Sir Putt-a-lot's
