The main advantages of Teensy 2.0 are strong 5 volt output signals and better compatibility with obscure Arduino libraries that have hard-coded dependencies on AVR timers. If you find such a library that doesn't compile or work with Teensy3, please do post a detailed message (and search this forum... many of them are already fixed). Teensy 2.0 is also slightly smaller and a few dollars cheaper.
Teensy++ 2.0 has a LOT of pins, which can be useful for building MIDI controllers and other projects where you want to connect a lot of stuff. There are many complex ways to connect many signals to a small number of pins on the smaller boards, but if you're just trying to just a project working, the simplest approach is to just get the board with enough I/O pins.