They are really different products. Chessbase is a game database management tool, while Aquarium is an interface for a chess engine. A better comparison would be Chess Assistant vs Chessbase, or Fritz interface vs Aquarium. Chessbase unfortunately does not include Fritz, and to do automated game analysis you need the Fritz product or one of the other engine products that Chessbase sells.
Aquarium is a brand new product so it is going to have some growing pains, but they have some very interesting ideas for making a nice analysis environment for serious users. They also work really closely with the Rybka team. I will hopefully be getting Rybka w/ Aquarium over the holidays and can post more about it then.
You are able to interactively analyze games within chessbase using chess engines, and it has much more powerful database features than what is available in the Fritz interface. I don't know what kind of database capabilities Aquarium has, but I imagine it is more limited than Chess Assistant as well.
Can any recommend to me which is better at the premium level?
I have Chessbase Light 2007 and like it a lot but obviously can't save anything which has proved troublesome as I have just found out recently. I hear Aquarium is better for analysis but is harder to use.
Also while I'm here, what's the difference between purchasing Chessbase (which includes Fritz 11 I believe) and Fritz by itself?