Here's my experience.
PS2 spans a pretty long delivery period. Earliest have the 5v boards that can fail and later PS2 has the 3v which are more reliable so it's good to ask or check the model year on the MTH website.
Sound is better with PS3 although some PS2's can have very good sound.
For steam engines, the PS3 wireless tether can come loose although there are easy fixes for this. Keep this in mind if you run your engines hard.
Pretty sure all PS3's have LED lamps and are much brighter than the PS2 lamps.
In general my PS2 fleet smokes better than my PS3's. Diesels and Steam.
I run DCS and Legacy together and have noticed that the PS3's can be fickle when a Legacy engine is on the track. No problem with the PS2's.
Crew talk sounds. On some of my PS2's diesels, the crew talk sounds like its recorded from real world dialogue. I like it. On my latest PS3's it sounds like two MTH employees reading from a script. Ugh.
If you are buying used engines, keep in mind that a used PS2 may need a new battery, new traction tires, lubrication and a really good cleaning to get it the way you want. This is less likely with a used PS3.