I used to be all for 3 stock matches because it just felt more dynamic and such. More can happen, will happen, etc. But when my scene switched over to 2 stock matches, I started to understand the appeal. The one big thing that I enjoy about 2 stock matches is that it's MUCH less mentally straining. Going to winners, then sent to losers, then making it to grands and reseting the bracket is ridiculous on that player (I haven't done this myself but I have made it to winners finals then losers finals). Hell, a Bo5 that goes to game 5 is a lot to keep up with when you're playing with 3 stocks. The other problem with 3 stock matches is when a character has a bad match-up, they can make it go for a really, really long time. As of late I find 2 stocks pretty appropriate these days. I find it more entertaining to watch, however when it comes to playing I'm all for 3 stock. I'm not really for either side as of now, but if I had to choose, I feel like I'm more for 2 stocks...at least more than I used to be. Though that could be because it's what I'm used to.
I did want to bring up one more point. A lot of people like to use the argument, "If you mess up early on, you're basically screwed cause you're down an entire stock." Hate to say it but that's the way it should be. In Street Fighter and other big fighters, it you mess up you lose like half (if not more) of your life guage. It's not a game of second chances, it's a game meant to be played by the best. If you SD enough that it's a problem that you need to bring up, you aren't ready to be playing at a top level.