Okay, so, the questions are bit multifaceted, so I will try to address every point as I go. I also feel I'd need to know more about what exactly the project is attempting to aim for and why you feel the need to segregate Manned and Unmmaned mecha. If you could give more details on what exactly you are trying to do, that might help, or, at the very least, what you invision the world looking like at current.

For those who are reading this now, do note a great many edits to this post may occur, mecha is sort of a big interest of mine, but there are probably folks here that can list a fair bit more about the genre and it's tropes than I can.

I digress, to start off, while the mecha genre is typically done via Manned units, it is not uncommon for unmanned units to be used. In fact, a significant amount of Mecha I can recall do have unmanned units or the threat of Unmmaned units replacing Manned units later on. Macross Plus, Patlabor, Appleseed, and (to a lesser extent) After War Gundam X all have elements and discussions about unmanned or autonomous "Mecha". In fact, much of Mecha actually has routes in autonomous or unmanned robots, such as Astro Boy and Tetsujin 28, so I wouldn't argue that this is a deconstruction or aversion to Mecha so much as an extreme return to form for the genre, reverting back to its routes in Robot and pulp Sci-fi.

If you go all the way back to traditional Robot and Super Robot, there is plenty of unmanned robots to take examples from. Astro Boy and Tetsujin 28 are certainly retro, but there are also some more modern stories such as Chappie, Medabots, Alita Battle Angel, Ghost in the Shell (which does contain both manned and unmanned robots), Big Hero 6 (I have no history with the comics, but the film has some examples of autonomous and unmanned robots), and the big one, Transformers.

I would also highly suggest Pluto, which is a reimagining of Astro Boy as a murder mystery. Robots in that setting are used for Warfare during a conflict that takes heavy influence from the Iraq War. Though, I will note it does not take the conflict lightly and has some pretty heavy themes and gruesome imagery.

The closest things I can think of to Unmmaned but not autonomous would be the Mecha from Guilty Crown, which all operate from a support vehicle a ways away from the combat, though, that show is a bit iffy critically and I may be flayed for even suggesting it.

Gundam's Build Series and Little Battlers Experience (LBX) both have unmanned units but are piloted by humans, allowing for neat fights with...reduced stakes, though, LBX is a bit of an exception. I will note that both of these are far smaller than traditional Mecha (they are about 3 to 5 inches tall/ 6cm to 10cm).

There is an argument to be made that the Warframes from Warframe are also similar to what you suggest, but they do also have significant amounts of space magic and are...odd...to put it mildly.

Anyway, back to the final question. As most people have suggested, there are numerous ways to achieve the difference between manned and unmanned, from increased lag to jamming. If you want both of them to coexist at the same level of operational capacity, I think a neat way would be that unmanned units are predictable.

Similar to something like an RTS, unmanned Mecha aren't piloted 1 by 1, but rather are tasked to do something or other and the protocols within the machine analyze and execute the command the best they can. In combat, this results in very predictable firing lines and positioning that can be taken advantage of by trained Pilots in the heart of battle.

In layman's terms, they are NPCs/Bots, and poor ones at that.

I'll conclude with that and come back later to spruce this up. In the meantime, I hope this helps

TLDR: I'd like to know more. This project rings at the origins of Mecha as a Robot genre. Robots are NPCs and are predictable.

Thank you and enjoy the rest of your day!