Not sure if you are ignoring the context of the situation or can't see it. We have a character, that from his very conception, is absolutely broken. People min-maxed Int/Tech in a way I am almost certain the QM didn't expect. Otherwise I doubt he would have done things like included the Counter power, which is already a very versatile skill, or have started us out as basically a superpowered goon. With the stats Nathan has, near any problem only needs time before he makes something to solve it. There is almost nothing out of reach and he only needs the tech base to springboard off of. Infrastructure is already covered with Luthor backing him up.
Rushing that development by handing out stats does incentivise doing things, but it comes at the cost of trivializing upcoming threats. I agree that there should be incentives for doing things, or at the very least punishments for turtling up, but this is not the way to go about it. If Nathan weren't a super genius, or if his main ability was growth, it would be reasonable. That's not the case when three weeks in the supergenius already has nanomachines and a tech tree that let's him surpass his physical deficiencies and is on his way towards unlocking more actions. The only part of this quest we're going to have trouble with is the beginning when he is average at everything while notable characters have more skill than him. Giving free stats lifts us out of that zone, and rushes his development. Even if we don't get free stats beyond a certain point, getting us out of that early funk is a problem. It catalyses that growth.
You see a gang fight and think that it was a close call. I see three weeks of work already putting us nearly beyond every mook we meet despite starting at the same skill level as them. We get Nanomachines-Armstrong Defense and mooks that aren't equipped with high tech are going to be incapable of harming us. Yes, superheroes have greater bonuses, but we're going to end up there eventually before going even further beyond. There's the big problem. Where do you see this quest going when Nathan starts being able to regularly win against the YJ team? Should the 16 year old start going toe to toe with the Justice League, and if so, what happens when he avoids them? How will the QM make reasonable challenges if we're smart about it?
At the start we should be taking more loses than wins because our character was designed to be really, really good at a specific thing before growing exponentially. We might lose a fight with Robin, but Robin cannot improve like we can. We might lose four fights against Robin, or ten, but in the end we're going to surpass him in a way he is incapable of matching. Mechanically, regardless of how good his athletics, fighting, or acrobatics are his stats will never rise above 8. The bonuses from his gear are going to be similarly outmatched, as we make better stuff, or can improve it further than he can. Even if he loots our gear and develops a counter to our nanomachines, all we have to do is look at one of his teammates and gain a new power on top of how we might advance ourselves or develop gear in the time between fights. It is insane growth.
I don't know how to make it clearer that while most of our opponents are going to be largely static, or will hit a peak, we aren't and won't. Even if they start improving to match us, they aren't going to be able to because we have one of the greatest minds in the setting. We're capable of looking at any looted tech regardless of how advanced (be reasonable, I don't expect him to deconstruct power rings or the like) and incorporating it into our own gear.
If it were just a chunk of xp automatically sent towards raising that stat, I'd be much less critical. But full levels for a 5% chance every roll we make in these events is crazy. Three rolls an update is a very low estimate that's also unintentionally misleading. If we're tasked with guarding a facility, and YJ shows up, there are going to be far more than three rolls unless we do very poorly.
