I know people in 2-year, 2.5-year, and 3-year programs who are required to do a Masters. I can't remember the exact figures, but I think most (~60-70%) programs require a Masters. I would guess that on average the research project done at a 3-year program is slightly more involved than the average one completed at a 2-year school. However, there is so much variation between schools.
For example, I know residents at a 2.5-year program who routinely complete a "whimpy" Masters. Their projects can't be any tougher than those undertaken at a program w/ shorter length (2 years). In fact, some of the 2-year program directors expect the most and work you pretty hard. I'm not saying that is bad, you just have to decide what you want. But if you wish, you can choose to do elaborate, time-intensive projects anywhere.
So, why do the directors make the kids stay for 3 vs. 2 years? My guesses: 1) to have the freedom to schedule in more research time during the week (likely not always used to do research by the residents) and 2) to allow the residents more time to complete more cases.
I bet most residents come out w/in a narrow range of each other. Many 2-year schools are very clinical because they have to be. They don't have you for 3 years. Yet, so much is dependent on the individual resident. So much of what we do is self-learning. I've discovered that you finish residency w/ whatever you want in your tank. Each school will provide you w/ an adequate number of patients to get you to a sufficient level. What you choose to do from there is up to you. No surprise. Life is what you make of it.