As an MS1 at a non-MSTP (though we applied this year) school I have to say that I have not seen any real differences from friends who are at MSTP schools.
One of the perks, I think, is the ability of the program to stay as small as it wants to. I know that sounds weird, but there is a lot to be said for being "taken care of" by the program administration. Sometimes having that extra funding, or a different source of funding, puts pressure on the program to grow, and while that is often good, it isn't always good.
In terms of time to get out -- i think that even some MSTP's are slow and some MD/PhD's get people out reasonably. I know my program puts a priority on progress and getting out, but that is just here. i think that is helped by the fact that its a relatively small program so they can keep track of us, and our mentors, all the time.
also, i think it depends where the program is. Here in Utah, the university is really the center of science in this region. we are not at all saturated like some other eastern cities. so the lack of MSTP here doesnt really seem to have an effect, because this institution is huge, extremely well funded, scientifically innovative, and very prestigious (we east coasters just dont hear about it, i think).
so, the bottom line is that it seems to depend on where you are if the non-MSTP really makes your life, as the student, different. i would check one thing for sure wherever you go -- find out what happens for YOUR funding if your mentor loses his. most good schools make sure that you stay supported, either through the grad school, the department or something else. but watch your own butt no matter what you hear through the grapevine.