Operationally, the differences between PS/2 and PS/3 are pretty small. PS/3 sound is typically somewhat better in quality, but it doesn't have nearly the volume of PS/2. (Only important if you are running engines in a club setting or other large layout with a lot of background noise).
However, there is a difference between the early version of PS/2 with a 5v motherboard and 9v battery and the later version with the 3v board and battery pack. Basically the early version is much less likely to be repairable if something goes wrong, due to the different configuration of the boards and the fact that the older boards are no longer available. No big deal if the price is right and it's been run so you know that it works, but something to think about on a NOS (New-old stock) item. There are a couple of guys on the OGR board who can work on the old boards, but most MTH dealers will not. They will want to upgrade to the later style board, which is expensive.