Python 3.x means lack of library support (ie, no PIL, NumPy, PyOpenGL, etc)
Still labeled as “Alpha” software, so it could be buggy
Old documentation/examples might not work for 2.5
Ability to use OpenGL to draw directly to the screen
API improvements (you don’t need as many logic bricks)
I’m currently using 2.5 for a game project and it’s working out pretty well. If you want, you can still do modeling and such in 2.49 and then import those into 2.5. However, I’d avoid doing animation this way.
There are more than likely more disadvantages/advantages to using 2.5 that I haven’t listed, but hopefully that will give you something to think about.
I noticed that animating meshes in 2.5 is a lot easier than the previous versions. This is a plus because you can animate water graphics straight into the game in about 4 minutes with all the necessary textures.