While I love playing 3D games I tend to produce in 2D more than 3D. The main reason is that 2D games have more longevity than 3D games. With 3D games you have a very short window to make your money in and after that your game is done. Your game will be graphically obsolete in a short span of time. On top of that, a revolutionary new paradigm could happen during production and make your product worthless. This has happened to me a couple of times.
There are other reasons why 3D isn't as "viral" as 2D. If your game is successful, people with make fun of it with cartoons or videos etc. This process is much easier if your game is in 2D. People can interact with it. With 3D this process is possible but it is much harder.
Lastly, the development is much more expensive. 3D artists are much fewer and more expensive. There are a lot more problems that can go wrong. The game could crash or something random can break your game. As a result you have to test them more. Even something as simple as collisions can be very problematic.
3D games are awesome and I love to play them. I am personally going to wait before I produce my 3D games. I will take a look at the production landscape before I start a game.