ok, i see we got a whole new thread here instead of myself and pathdr taking over the clinical experience thread
i think there are some other differences between MSTP and non-MSTP programs besides the funding. although, i do not consider prestige to be one of those differences, or even an issue, because as pathdr has brought up before, no one ever cares or mentions it once the degrees are completed.
1.) Funding: my program does not gaurantee funding during your graduate school only years, although there is a full tuition waiver for both med school and graduate school. we are gauranteed a minimum level of funding (i think about $7000) during our medical school years if our other fellowships will not cover it. however, everyone in our program who is an MD/PhD (not MD/JD or MD/MBA) is fully funded as of right now.
2.) Size of program: non-MSTPs tend to be larger since funding comes from other sources...my program accepted nearly 30 students last year, as compared to MSTPs which i think normally accept less than 10 (not sure though...) We have more than 175 total students in the program at this time.
3.) Flexibility: my program allows you to pursue a PhD in any subject area you chose, whereas MSTPs are usually limited to the basic sciences (biochem, biology, physiology, etc). we have students pursuing PhDs in latin studies, romance languages, ed psych, nutrition, english, any social science/humanities, as well as the major sciences.
4.) Order: we have to enter graduate school first. the majority of students decompress the M1 year over their 4/5 years of graduate school and then once the PhD is complete, do M2/3/4, although this is not set in stone.
I don't know whether most people see these differences as advantages or disadvantages.