Thanks DrMona... I admit, that's one thing I have not done well. Last year, my apps were out super late because I took the MCAT so late. In hindsight, I probably shouldn't have applied but alas, my anxiety to start med school got the better of me.
This year, the waitlist thing screwed me up. I didn't even hear a peep from either school until JUNE, and that was to tell me "hey congrats - you're waitlisted!" Gee thanks. So instead of being pessimistic but prepared, I was optimistic with no AMCAS at the starting gate. I didn't complete until mid-late August, even though I knew better.
This is also why I'm trying to figure out now what I need to do next year if I don't get in this year. If it does make sense to apply the third time, I will need to start preparing my strategy nowish. This may require dropping my full time job and going back to school full time (or doing both, not sure), or making other big changes sooner rather than later.
I fully understand your frustration about what to do next, especially when you are caught in that wait-list "no-man's land." I was wait-listed twice; I received my acceptance letter after being wait-listed the second time. The only difference in applying the 2nd time was that I got my AMCAS application submitted in July-August, and got an interview at the end of October -- on Halloween (very fitting). This time I was wait-listed in November.
By the next March I was pretty despondent, because I didn't know what else I could do that would make the difference with the admission's committee. I was about to plan for the next application season that would have started in 3 months. So I telephoned the director of admissions, who was originally from my home city, and from one of my alma maters. I asked him, "Can you tell me anything that I could do that would help get me an acceptance from your medical school for the next application season (instead of the "close, but no cigar" status)?
I will never forget that his response was "Well, let's not be so hasty in talking about the next application. The 'fat's still in the fire' for this year's acceptances. So don't give up for this year, just yet."
I still don't really know if he already knew something was going to change for me, or was just anticipating the events that always seem to take place before the first year med school class is finalized. However, on May 16th of that year I received a certified letter from the medical school, informing me that I was being offered an acceptance to that year's freshman class. I was practically in shock, since I had no idea that this acceptance letter would come through for that year.
Therefore, I am suggesting that you might call up anyone from the admissions committee of the respective med schools where you were waitlisted -- the most approachable person at each place may be the admissions liason rep or the director (or whomever you would feel most comfortable talking to). You can even take the approach that as a non-traditional applicant that you understand the evaluation process might be somewhat different -- could they tell you anything that would help to make you a stronger candidate for acceptance next time? You know that they must have liked your application, since they put you on the waitlist (at both schools).
Also be aware that some schools will play this game, especially with non-traditional applicants -- they want to see how much perseverance you have in going for this goal. In other words, they want to see if you will keep on trying, because you want to go to med school so badly, or will you give up after 1 or 2 times?
You have to ask YOURSELF, "how badly do I want to go to med school ? Am I willing to keep trying, and indicate to the admissions committee that I will not turn around and give up, without a fight?"
I have a doctor friend who was once a non-traditional applicant himself, who is now a successful and wealthy physician, and who is friends with one of the deans of the med school in my home city. My friend talked to this dean, and reported back to me what had been communicated to him about increasing the chances of acceptance. Again, this was the main theme that the dean had communicated to him -- how much does an applicant want to go to med school? Are they willing to go to any lengths to achieve it? Are they willing to show up every month, week or day, at the admissions office, basically indicating that they will keep trying until they get accepted?
My friend thought that I would eventually get accepted to this med school in my home city -- which would have made everything a lot simpler for my husband and me. For a long time I would not consider applying elsewhere because I couldn't see myself having to live apart from my husband (I didn't feel that it would be fair to ask my husband to move for med school and then move 4 years later for residency).
Nevertheless, another "advisor" asked me why I didn't consider the other state med school, which was about 500 miles away. When I started making excuses, this person asked me, "How badly do you really want to go to med school? Are you willing to try another state med school, that might actually be more willing to accept non-traditional applicants? If you got accepted at another med school, would you make the sacrifice to live away from your family for 4 years? Again, how badly do you want med school?
Therefore, I had to discuss it with my husband (who has always been my #1 fan and supporter) about what would happen if I got accepted to med school elsewhere. And we both knew the answer -- that there was no way that I could give up the chance to go to med school, even if it meant having to be apart from my husband for awhile. Because we both knew that I would not have been able to live with myself, if I were to give up that opportunity.
Well, as fate would have it, I got accepted at the med school 500 miles away from my home city. But my husband and I knew that we could work this out together -- that we could deal with being apart as long as it would only be for a temporary period of time.
I cannot tell you that this entire process has been easy -- there have been times that I questioned myself about why I ever wanted this (especially when things did not go the way I had planned). But even during the worst of times, there was that continual sense of empowerment that energized me to keep going forward with each day. That feeling of empowerment that came with living out your sought-after dream has been so robust that it has conquered any obstacle or difficulty that befell my path.
I realize that this has been a longer post than I originally had intended. But when I read your questions and concerns, I was reminded of my own questions about "how long was too long" to pursue this dream. Only you can answer these questions regarding how many times do you keep on applying. Just remember this: Don't let any other person convince you that you do not want to keep trying. If you have any further questions, please feel free to post them here in this thread or via private message.
Never give up on your dream!!! 
