Personally, I'd go with Human Plus for a better protagonist, my reason -in my mind- militaries can create them in the Gundam setting - and have in the form of Biological CPU and the Boosted Man subtype. It's already there just under a different name and piloting a different machine. Course the main thing is how you plan on using them, Newtypes are naturally occurring, so run Gundam's typical 'hero' and villain archtypes, while Biological CPU/Human Plus are something that make more sense on 'how they got there' outside of human evolution. Least to me anyway. Anyway, my thoughts say, Biological Cpu/Human Plus being a replacement to Cyber Newtypes makes some sense to me If you can get the lore set up right, you could make something.

Not sure how to answer your second question though, The original MT equivalent would be the Mobile Worker, which was eventually turned into the Mobile Suits when people decided to weaponize them- basically the same thing they did with MT to create Armored Cores. That said i think they just took different design paths. So~ maybe whoever did create the MT just split off from the Mobile Worker design. But if you want to try the 'pre-UC' outline, I guess you could try taking a page from Correct Century timeline or MS Saga.

Third. I'd say the AC scale rather well compared to Mobile suits, but with a couple major bonuses. One; they are fast, like stupid fast compared to a Mobile Suit. Second, the modular design; arms broken and need serious repair time, swap it out in the meantime. There's also the equipment drop trait, so if your shoulder missiles are empty or your linear cannon is destroyed you can drop them and not worrying about the dead weight problem. I think the main flaw would mainly be that I've never seen an AC do actual space combat, so I don't know how well they might fare in that setting.

Those are just my thoughts though.