I would say deciding on a RTR or KIT is a personal preference...I would say go for the kit because then you can have the fun of building your buggy up, you will know it inside and out from building it and you can make sure it's done right the first time!
As far as you spending about the same between the kits I would say is false, well that is if you already have a Tx/Rx to drop in it and if you already have other RC then you should have a sufficient servo laying around to drop in it. The only other thing is the body comes clear for you to paint versus getting one thats already done up. If you want to make this your Baja, then build it up and do it the way you want to. The servos are usually the first things your going to want to replace so go ahead and do it right the first time!
I bought my baja used, it was a first generation RTR. The guy had already invested quite a bit of money into the buggy but none-the-less it was still used and needed some TLC...I bought a manual off of ebay and the day I brought it home I tore it completely apart, cleaned everything, went through the motor and by the time I was ready to put it back together the manual had arrived in the mail. I just followed the build instructions in the manual and it all went back together in only a few hours. IMO its a fairly simple build!
Hope this helps ;-)