Prototypes are usually just that. Testbeds for new technologies. They get the weapons, the armor and the gimmicks and usually the top notch pilots to test their capabilities.

Its not cost effective to give everyone a gundam. Its expensive and the skills of the pilot aren't as impressive. Its also believed that with enough numbers even a small attack can be great. Overwhelm with numbers. They take what data they like from the prototypes and make the mass produced suits making them more cost effective. In a fight a mp suit is generally gonna be at the disadvantage. The prototypes have better armor "phase shift", better weapon arrangements. And you get the capable pilots.
Even thou Athrun was in the Zaku he managed to atleast mount some defense but he was little more than a nuisance inflicting practically zero damage. Then you see the offensive capabilities of the prototypes over powering the Zaku. Abyss's chest cannon ripping through the weak shield and armor.

Now if the three pilots hadn't retreated when they did the mp suits and Shinn would have overpowered them. The limited power supply of the batteries and constant drain via the Phase Shift would of left them helpless. So all the suits have a purpose. I hope that was alil helpful. Thats my whole 2 cents on that but to get specific.

The original five Gundams were as ^^ said. To give a suit to the naturals capable of competing with the coordinators. The suit's capabilities making up for the pilot's. These prototypes would provide the data on what worked best then they would design the massproduced. They seemed to like Strike's and Duel's data and fashioned the Daggers from that. Similiar to what was done in MSG. With the newer OS enabling naturals to pilot the MP suits just as well as a coordinator pilot they had an effective defense atleast against the MP suits. New prototypes would be needed for fighting more advanced suits. Its all basically a matter a cost versus combat effectiveness.