I prefer the Brainwave Deck, as, though it's a bit more complicated to perform, it's a much better effect. However, it's all about preference.
The Invisible Deck allows a spectator's selected card to show up as the only card face down in the deck. The Brainwave Deck allows a spectator's selected card to show up as the only card face up in the deck, with the back transforming to a different color -- it provides two effects, instead of one.
The Brainwave Deck is harder to find -- it's not rare, but rarer than the Invisible Deck. In a sense, it does has more substance and is more clean than the Invisible Deck.
Cheers,
JTM