This is a bit complicated. The basic difference between Proto 2.0 and 3.0 is that 3.0 doesn't use a battery, thereby eliminating many of the complaints about previous versions of Proto-Sound. Some Proto-3 units also have better sound quality than Proto-2, but this varies and is a matter of opinion. Some Proto-3 units don't produce much sound volume; others can be cranked up just as loud as Proto-2, if your operating environment demands it.
There are two versions of Proto-2. The earlier version used a 9v (actually 8.4v) rechargeable battery and is generally referred to as 5v Proto-2 because that is the internal voltage used on the boards. The later version uses a 3v battery pack and the internal voltage is also 3v. Replacement boards are not available for the 5v systems, but there are a couple of repair techs who can sometimes fix the early versions. You can replace the battery on either Proto-2 system with a gadget called a BCR, which is a capacitor bank that serves the same function as the battery.
As far as availability goes, it varies according to model. You will have to check the MTH website for whether each locomotive was available with Proto-2, Proto-3, or both. Unfortunately the website does not tell you which Proto-2 units are 5v and which are 3v, but you can get a rough idea from the date the unit was cataloged. I seem to remember the changeover was around 2005, but someone can correct me on that if my memory is faulty.