Ive installed hundreds of Aftermarket remote starters, but ive never done OEM ones. Im not sure on this, but in my 2003 Camry, my OEM starter is just clipped in.
The factory RS systems are not very hard to install. I have installed lots of the RS3000 systems in Gen3's. Pretty much everything si done in the drivers side kick panel. As for upgrading it is all up to you. The keyless entry is nothing more than a remote door unlocker. IF you want a full blown security system you will need to go aftermarket or have the RS system installed or do it yourself. FOr what you get I dont know that I would want to have the RS system installed unless you were buying the car new and could get it put in with the deal. You will probably pay several hundred dollars for the system and then the installation will not be cheap either. I would look for a good aftermarket system that will suit all of your needs.