first of all - don't worry, you're not alone - i was ready to give up on the DW thing altogether because i didn't know how to choose a location!
here is why I chose my location (Las Caletas/Puerto Vallarta)
1) we knew we were honeymooning in Hawaii - so we wanted that side of the world, we looked at western Mexico (Cabo, PV, etc.) and S. California
2) i didn't want to get married at a big resort where everyone could be watching and walking by, i wanted more private
3) we wanted a ceremony and reception on the beach
4) PV is a little cheaper than Cabo
5) as for where to stay (Dreams PV) - we wanted an all-inclusive, just to make the planning a tad easier, and have everyone in one place (other than a few guests)
6) Dreams prices ($106-129/night/person) weren't bad in comparision to other resorts for what you get and they have a great reputation
... i'm sure there's more ...