I don't know if this counts as troubleshooting, but I having a difficult time deciding which one I will use for a project. Which one?
It depends what kind of project you're working on. I'm not gonna list the advantages and disadvantages off each, a google search should find that for you.
Try both and see which you prefer.
I googled it, but I still don't know which one to pick...
Although I'm probably going to use Rm2k3...
First off, what sorta project are you making?
Secondly, if it's a choice between two RPG makers, just go for the one you have more experience with, or the one you are more comfortable with.
Actually, experience and comfort are two things you should look for first - What sorta project your making should be a close second when you are deciding.