FireRed generally has the best compatibility with tools as well as lots of documentations, not to mention JPAN's engine and Jambo51's upcoming 649 Patch so most people look to hack it initially. I would say that Emerald is on average used by more advanced hackers as they have a lot more to figure out/ explore and there isn't as much free space available to expand upon. Since it is your first hack I would suggest trying out FireRed as there is far more information to guide you and move on to Emerald in the future if you feel like doing so.
Well I was thinking about making a mod. for on the 3rd gen Pokemon games but I am not sure which would work out best. My first choice was Emerald but I am not sure which would be easier to work with of the 3 games. Keep in mind this would be my first hack/mod so I want to make it pretty good.
EDIT: hopefully you see this edit before you post again but actually I am thinking I may be better off helping someone before I attempt my own project.