You're right that it's the biggest question. I was mistaken to not ask myself the "why do I want to be a scientist" question after undergrad; the road after grad school into academia or industry is long as well, and I shouldn't have started without realizing I probably wouldn't like the end result. I think a big part of that mistake was my assumption that I wouldn't have to be a scientist if I went to grad school. I obviously was deluding myself; although alternative career paths exist, there are almost always better ways of getting there instead of through a PhD program, and I wonder if having a PhD will necessarily give me an edge in non-research careers. (Although at this point, I'm very hesitant to just quit my PhD program.)
Right now I can say why I don't want to be a scientist and perhaps why a doctor or physician scientist might be a better fit. I dislike the lack of human contact and communication in the daily lab environment. I derive very little personal satisfaction in doing my project (which is basic science, with little to no clinical or practical relevance). The prospect of having to manage or come up with similar projects of my own in the future and sell their virtues to others for funding makes me feel like a fraud. I really enjoy learning about science, reading about new discoveries and teaching others what I know, but actually doing basic science and planning new experiments doesn't give me any joy. I ask myself all the time why I or anyone else should care about what I'm doing. I feel all this, and I can't even say the reason is that my project is currently failing (though of course it could at any moment).
I can live with this for the next few years, but when I've started to think about the future (postdoc, maybe 2 postdocs as is becoming common in the biosciences, then trying for a faculty or staff scientist position and possibly doing research for the rest of my life), I start experiencing something of a panicky crisis. I think I've known that research is not a career I would really enjoy, but went to grad school anyway. Sounds stupid, and it is, but unfortunately I realize this a little late. Hopefully, it's not too, too late...
One small thing that made me think about if I should look seriously at medicine is that I find myself enjoying performing surgeries (my project involves animals), and find myself more interested in and rewarded by the surgical process and how the animals fare afterwards than the experiments and data I get from the surgeries. Of course, I also realize working with animals and people are totally different; I need to collect more information about clinical life before I can actually give reasons why I want to be a doctor.
I'd love to hear any more thoughts or advice from people who've chosen to go for an MD after starting/finishing their PhD. Just to know you guys are out there is encouraging.