There are a few difference between OTC and Nike Oregon Project. First of all, technically, there is no more Oregon Project, it is all called Oregon Track Club. But, the original Oregon Track Club Elite is based out of Eugene, Nick Symmonds, Will Leer, Russel Brown, and others, those guys are for the most part a "b" team of Nike athletes (minus symmonds of course). They are all very good, but it's an environment for guys who probably would not have contracts without the group. The Eugene group is also mostly middle distance focused, there are some 5k 10k steeple guys, but it's 800 heavy.
The Portland group is coached by either Salazar or Schumaker, These guys are either transfers from the Wisconsin group (Teg Solinsky, Jager), Salazar Athletes (Rupp, Gouchers, Ritz), or Nike athletes that are high profile and were under performing so were forced to move to Salazar or lose the contract (Webb, maybe Ritz).
There are Nike athletes living in the states that don't run with either of these Groups, World Champs Qualifier Kyle Alcorn comes to mind first, who knows how long this will be the case.
To answer the original question, at least this year, the Portland group is by far teh best at least this year. They swept the Mens 10k, the Mens 5k, and had Begely and Goucher on the Women's side.