Well just because you're not directly controlling doesn't mean you have no control over the mech and the presiding encounter. You'd just take the Captain Picard role you know? He doesn't directly control the Enterprise but instead he commands it.
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While that’s certainly feasible, that’s not what’s happening in this case. You aren’t the sidekick’s commander or anything. You could offer her advice, but ultimately it’d be up to her if she wanted to listen. The player controlling the mech would 100% be just a gameplay thing, no lore explanation at all.