I think there is reason to have pilots and I have ideas that could give the feature more merit.
But I never wanted pilots in the first place because I think there's better reason to have never added them in the first place. Pilots can maybe add an element of unpredictability to the game but with features like this the reality sometimes ends up being another part of the game a META forms around (right now META is stalker, rocket mortar, fei, rm radius, rm damage, stalker ability damage bonus. And if that happens, well the feature lacks any merit. Another thing is, the best source of unpredictability is the players themselves.
But since the feature is here there are a couple things that would help it. First of all, SWAPPING IMPLANTS! I don't want to scrap my implant just to move it to another pilot. Players like to play around with their builds and making us scrap our upgraded implants if we want to move them restricts player freedom. Allowing us to swap upgraded implants will increase player freedom and give the feature more merit. Second is pilots which give HP to mechs based on class. There's a whole lot of extra damage in the arena nowadays and not a lot of extra HP. We've also got the problem of innate skills only for weapon classes is promoting cookie-cutter builds and discouraging hybrid builds. So pilots for mech HP will solve 2 current problems. Again giving the feature more merit. Oh and remove rocket mortar radius implant from the game. That's it, remove it and compensate players who purchased and upgraded it. It's a completely unnecessary buff to the weapon. The maps you made up until pilots had been balanced around rocket mortars without that radius buff. To re-balance the implant, you would have to overhaul your maps.