Let's review their abilities:

The Prototype:

is huge, it's fast, it can go almost as fast as a train, it's a spider, it can climb walls, its hands are sharp and it could kill anyone with them, it's very strong, it can break through the walls of a giant house, it survived a train crash, and it's apparently intelligent, but it didn't kill the protagonist.

The Mimic:

can change size, can assemble itself, it's somewhat fast, it could catch up to Edwin in a moving car, it can literally get into any suit and control it, it's strong, it can open electric doors (like the ones in FNaF 1), and it survived being inside lava (molten metal), being hit by a car, until debris fell on it, and even then, Mimic did kill the protagonist.

Well, it's hard to say who would win because both are strong and have their advantages. The prototype is big and strong, but Mimic is fast and can control suits

but I Think Mimic has many more abilities and advantages to win.

The Mimic could literally get inside the Prototype and control it, right?

I find this debate fun, but seeing that many people think the Prototype wins just because people see Mimic as “just an endoeskeleton” only shows that he is very underrated.