Well, I'll share at the cost of my own embarrassment - but I too was looking for such candid experiences when I was applying so here goes. I went to a good school but got horrible grades, partially due to just being plain dumb (more specifically being too young and as an extension too immature for college, I will never let my kids skip grades). My undergrad GPA is appalling even for bottom-tier MD-only tracks (it's a 3.0). My MCAT I took a few times, got sub 30 my first try out, but finally pulled a 33. I applied to MD-only in 2003ish and got nothing, no interviews, no nada. With enthusiasm waning for med school, I went and got a Master's degree (non-special, traditional Masters) at a top 10 med school that I could use outside of being a doctor. Did really well (near 4.0) to show that I could hack school (and even tutored some MDs) but also developed a fine professional career in healthcare.
This year I applied to about 25 MD/PhD programs, both MSTP and non-MSTP all across the gamut (from Harvard down to the smallest of programs), received 1 MSTP interview and was waitlisted, and ultimately pseudo-rejected. I have no hard evidence but I'm convinced i was in maybe the top 2 of the waitlist of a small MSTP program.
I think my only strength throughout has been my research. I have 9 publications, 1 first author. I've researched up the wazzoo. The other thing is I've worked in a myriad of positions along all of healthcare and the Dean of the School that I interviewed with made special comment about this - he thought this was my biggest strength and not my research (We have a bunch of 22 year olds who have never paid a single dollar for healthcare in their life.. and we expect them to understand the foibles of our healthcare system? and somehow incite change to it? - i found this to be a very insightful topic of conversation and something I never considered in my candidacy). The same dean also made indirect comments that he was fully aware of the weaknesses in my GPA but saw my potential contributions and insights as outweighing these things.
So what I hope to convey is what neuronix and CCLCMer have said, which is approach this whole process with realism, but do so with a fervor and a full-head of steam and energy. Ultimately I was close but not quite there for MD/PhD. I am, however, going to medical school (accepted MD only) and with any luck, may get into the MSTP as an internal applicant next year.
Would I have gone ahead and applied knowing the full breadth of emotions I had to go through for the last X years? Ugh.... I have to say it's been more than brutal. BUT, the answer would be I would do it all again, because I'm going to be a doctor and I can make it as research-intense as I want. I was a borderline MD-only candidate and now I have a chance to do some great things either as an MD or MD/PhD at a fine school.
Recognize that you have a tough battle, but there's no need to distinguish between "no chance" and "low chance" or even "application-worthy chance". I got 1 acceptance and that was all I needed to be on the path to physician scientist... of some sort.