The two decks are entirely different things. The Stripper deck has many applications to it. It can be used for so many different things, and it is a great gaff deck, and it can be actually examined by the spectators, (of course not the TOO observant ones). If you are thinking that the effects produced by a Stripper deck are weak in nature, I suggest thinking again because there are some incredible things you can do with a Stripper Deck like a great variation of Triumph, where you can actually let the spectator shuffle the cards and mix them up, and you can actually spread to show the mix. I have been using that for a long time, but the basic application can be found on Sankey Secret Files (under 180 Degrees, although I'm sure it has been thought of by many more people before Sankey).
On the other hand, the Brainwave deck, though powerful in nature for its mentalism sort of feel, it can only accomplish one basic effect, and it has a sort of anti-climax to it - I don't like the addition of the different colored back. It is better to stick with the Invisible Deck. The main effect is supposed to be that the card is turned over in the deck and that's all. The extra climax somehow, no matter how wierd it seems, may actually weaken the effect in a way, and raise uncalled suspicion from your spectators.
The opinions vary from individual to individual. I, myself, prefer the Stripper deck because of the multiple uses that it has and, of course, for one of the greatest versions of Triumph that leaves spectators gaping. I don't use the Brainwave deck a lot, but sometimes I do use the invisible Deck which usually gains a much better reaction.