I have both units, so I can comment on one vs. another.
Bodies/Shells:
The Proto 1000 is a very nicely detailed shell that was released about 5 or 6 years after the Stewart shells had been released (iirc). Detailing is about on par with the Stewart offering, but aside from the cast-on handrails and grab irons that were mentioned previously, I can only think of a few detail differences.
First off, the Stewart has nice fan detail if a little shallow. The P1K shell has nice fan shrouds of the correct height but the grilles are incorrect and have no fan detail through the mesh.
Secondly, the Stewart shell has sharper rivet detail and correct numberboards. The P1K numberboards do not stand out as far as they should (realize that it is not a very noticeable discrepancy), but the reasons for that I think are because the Stewart shell uses separate numberboards vs. the cast-on P1K piece.
Third, the P1K shell has deeper "chicken wire" than the Stewart shell. This is a toss-up as from a foot away you can barely notice the difference, however during weathering or painting it may make it necessary to use a finer brush when painting the vents on the side.
Also, the Stewart has an option of dynamic vs. non dynamic brakes, where the P1K is available non-dynamic only.
Drives:
The Stewart uses a Kato drive which is very quiet and powerful, but the P1K has a huge frame which weighs a ton and the proven Athearn style powertrain. Proper break-in (which has been covered again and again at this site) of the P1K will result in a loco that is almost as quiet as the Kato.
The only problem I have with the drive is a detail one: the P1K uses the P2K sideframes which are not as detailed as the Kato, however simply swapping them with Athearn Blomberg sideframes will result in a good detail upgrade.
My verdict:
The P1K is about on par with the Stewart detail wise, the Stewart edges out the P1K in performance. However, when you can get a P1K on Ebay for 20 bucks vs. 50 or more for the Stewart, the P1K starts to look better and better.
It will likely take the same amount of time to make a good representation of your favorite F3 with either offering. The P1K will need the handrails and grabs cut off, and both will need drilling and the odd bit of sanding, especially around the nose contour to remove mold marks.
"What was it the engines said?
Pilots touching, head to head,
half a world behind each back?
'They should have made this double track'"