I have both and aside from ads, there are no differences.
However, Fuelly has stated in the past that new version of Gas Cubby (which may or may not be called Gas Cubby) may not necessarily be a free upgrade. So I would hold off until Fuelly clarifies.
Gas Cubby will be renamed for Gas Fuelly (and eventually just Fuelly), and it will be a full rewrite for iOS 7. Initially, the app may not add new features.
There will be free (ad supported) and paid version (ad free). Paid version will likely have additional features.