Downplayed: Zero is better than the Mk. I units in performance, but not by enough to matter in most cases.
Troperion Zero is an ancient alien starfighter from which reverse enginereed technology has been used to create the Mk. I units. A lot of its technology still is too advanced (or expensive) to be replicated, and a lot more remains beyond human understanding.
MP units are cloned/copied from Troperion Zero. Thanks to the Clone Degeneration, MP units lose the powers that the original had, or they get defects like lower endurance, etc.
Few people can actually pilot Troperion Zero, so the mass-production model was adjusted to actually be within most people's ability to pilot.
The company making the prototype sunk all their resources into it, and upon getting a production contract, they cut corners to secure a greater profit for themselves, or to get more built in a shorter amount of time.
There are many technologies and gadgets that, while nice in theory, are not practical for field use for various reasons (cost, reliability, the ability to withstand often harsh field conditions, ease of repair, etc.) so while they're present in the prototype, they're removed or replaced with less capable versions for the mass production model.
Subverted: Troperion Zero shows signs of being a Super Prototype, including a distinctive appearance and an unique weapon, but it turns to be inferior to Troperion Mk. I. The thing making it stand out is the sheer ability of its pilot, Alion Landstar.
Double Subverted: On a battle against a hi-jacked Mk. I unit, Alion starts losing his edge quickly due the high power breach between the machines. But then he engages into Zero's Maximum-Overdrive, an unique function absent from the Mk. I that overpowers completely the stolen unit.
Combat wise, Troperion Zero doesn't appear to be too superior to the Mk. I units, but closer inspection reveals it has some awesome pilot commodities integrated; like leather seats, hi-fidelity audio systems and a mini-bar. All that Mk. I units have is a extremely uncomfortable cockpit and AM radio.
Zero's main weapon is a BFG capable of one-hit-killing almost everything that dares to cross its path. Mk. I's main weapon is a measly squirt gun that actually deals more damage when thrown than when used "properly".
Zig Zagged: The contrast between prototypes and MP units varies wildly on this series. While Troperion Zero is way superior to the Mk. I, the Subvertron Alpha is rather subpar when compared to the mass-produced Subvertron Beta. Meanwhile, the Proto-Devarium is roughly on par with its MP brothers...
Averted: Prototype mechas don't particularly exceed its MP versions performance; most of them don't even get to see a real combat anyway.
Enforced: "The show title is 'Troperion Zero: Chronicles of the Trope Wars' after all folks; the titular machine wouldn't look too impressive if it is out-classed by its little brothers. (and that would hurt the model kits sales, too)"
Lampshaded: "Unit Zero's specifications are outstanding. Will the Mk. I units be on par with it?" "Unfortunately, no. However, that's actually a blessing in disguise: This machine is so powerful that it would kill most of its pilots if not careful. Only super-men can control this beast."
Invoked: The prototype is intended not only to create new line of mecha, but also as a mobile platform for testing advanced weapons in real combat. Troperion Zero is jam-packed with costly experimental tech, built out of finest materials, and armaments are hot-swappable (which also just happens to increase amounts of merchandise).
Defied: The creator's of the Troperion Zero try as hard as they can to make the Troperion Mk. I just as good as the prototype.
Conversed: "If they could make a one-off prototype as powerful as the Troperion Zero, why couldn't they mass-produce it?"
While Troperion Zero's specs and weaponry are more potent than its MP counterparts, the experimental nature of the unit also makes it more unreliable, being more susceptible to malfunction than the tested Mk. I units. It's also almost impossible to maintain or repair due the unique nature of its components. It ends as a museum piece or as scrap-metal after a few battles, something that wasn't intended to begin with.
Troperion Zero really is superior to the Mk. I from a raw performance standpoint, not substantially more prone to failure, and can use many of the same parts. However, the human pilot is physically incapable of safely handling Troperion Zero. The thrusters which vastly exceed the production models, making it fully three times faster? The incredible G-forces they produce also cause brain aneurysms in pilots. The Mk. I's improved safety features mean that, in spite of lower peak performance, it's capable of moving faster and hitting harder without endangering the pilot; after the Ace Pilot is killed in action when the Wave Motion Gun's recoil tears his arm off, the Troperion Zero is put into storage, never to be used again...
Then, as enemy knocks on a door, Troperion Zero is promptly recommissioned from the museum. In the meantime, one particularly enthusiastic keeper of said museum ironed out most bugs and defects.
...until the Hero's Training from Hell enables him to eventually withstand the enormous physical demands of the machine, and so it's brought back into service as his personal unit.
Back to Super Prototype, but fair warning: we had to lower the specs a bit to make it work in the real world.