Here's the recommendations I give to third year students:
1) How important are procedures to your life? Obviously it's a major dividing line and something that you MUST figure out because it puts you on a surgical path if it's your overwhelming concern. Being a "doer" though can mean lots of different things to different people.
2) What types of patients do you want to see - Adults vs kids, mostly healthy vs lots of problems, women vs men? Again, obvious difference and puts you on specific paths
3) Outpatient vs inpatient - or how much do you like clinic? This is tougher, but also important, particularly once you've gotten past items 1 and 2. Certainly this is a major difference between Critical Care and endocrinology in either peds or medicine.
4) When you say "doer" what do you mean? Some people love diagnosis, some people love being a manager (in either the short - ICU - or long term - general medicine [diabetes] or peds [ADHD]), and some people are treaters.
5) Do you want to know one system extremely well, or know a little about a lot of systems. For me, I'm looking to go into Peds Critical Care, and the appeal of dealing with lots of different body systems is one of my favorite aspects of the field. Other people want to focus on one organ and give two licks about the rest. What do you prefer?
6) Along the lines of #5, remember that every specialty has it's 5 things that you see over and over and OVER again. Can you find the field where you don't mind those five things waking you up at 3 in the morning?
I think that GI and OB/GYN actually do have a lot of similarities, and so it's not that surprising you think both are good fits. Both have a nice combination of inpatient/outpatient issues, have procedural aspects, and provide the opportunity for some significant continuity of care. You can really develop some strong relationships and provide significant levels of care to make your patient's life better in both fields.
And before you get the onslaught of people hating on OB/GYN because of the residents' cattiness, being male will help a lot.
Good luck with your decision.