I have a number of Proto2000 and Proto1000 engines, and all have received dcc "motor-only" decoders.
I'm not interested much in sound, only good running quality.
On some of them (particularly Proto1000's), dcc is easy to install. (RS11's and RS2's)
I remove the factory light board (even if it has an 8-pin decoder slot), and install a Soundtraxx MC2H104at. Wires all match up. Sometimes I keep the original incandescant headlights, sometime I replace them with LED's.
The Proto2000's -- at least SOME of the older runs -- are a bit more tricky to get a dcc board into, because there isn't enough room at the top of the engine weight to fit a decoder, unless you get a small one (without pins) and hand-solder it together (and even then, it can be tight). But it still can be done. This affects some of the earliest GP7/GP9 runs. This can be more problematic with sound -- you might need to machine down the internal weights in order to get sufficient room for speakers.
Just about ALL the Proto 4-axle engines are going to need axle gear replacements. I buy pre-assembled Athearn or Walthers 40" wheelsets and change them out.
I have a few Proto2000 SD's, the gears seem fine in these -- no replacement needed.
You WILL need to completely disassemble some of these, in order to get at all the gears, gear towers, worms, bearings -- to clean out the old, now-pasty, lube (it's like peanut butter). Some I've bought were ok, but most need some cleaning.
Once cleaned up and with dcc, my Proto2000/1000 engines are some of my best -- and most SILENT -- runners. Smooth low-speed operation, too.