To give the opposing viewpoint, I would be pretty upset if after a full 4-5 years of doing research they made me do the 4th year research project. At Penn, MD/PhDs are exempt from that requirement and alot of schools don't have that requirement at all. If you care about these sorts of things, look into these things when you're applying to med schools. Some of the schools still have some 6 month rural medicine requirement for MD/PhDs. Seems kind of silly considering extremely few MD/PhDs end up doing that sort of thing.
In my opinion, It's simply the old mindset that MD/PhDs should be getting the FULL MD and PhD and not trying to integrate. It's also that MD/PhD programs often times don't want to step on anyone's toes, so everyone takes that attitude: what's another 6 months for these extra requirements? We don't want to make the med school or the grad school angry, so what's 8 years matter vs. 7 years in the grand scheme of things? You definately see it in the students here when they're faced with something they don't like. We're powerless to change it (not true), it'll look bad if we say anything, so we'll just make the best of it and if any applicants ask us we'll just put on a smiley face and spin some nonsense we don't believe.
Hurricane, I don't know where you go to school, but my impression is that you pretty much have to take a full 4th year. I'm willing to bet the average graduation time is more like 8 years (or more?) there. In the end, my message here isn't to say "My way is better than your way", but rather to encourage applicants to make up their own minds about integration. Do you want to spend 8-9 years getting the "full" MD and PhD experience (as one MD/PhD director explained to me) or do you want to spend 7-8 years with with some requirements taken out? There's always that argument, "some students take longer for personal reasons" or "some students work harder than others" or "luck" and all that crap. Yes, that all comes out in the wash. It's why some programs have average graduation times around 7.3 years, and some are up in the 8.5 range. Decide for yourself.