Well in all fairness just about every video game has some variation of this very same problem. Particularly when it comes to RPGs, protagonists very unrealistically learn and become experts in a whole bunch of areas that would normally take decades for human beings to become adept at.
In any Fallout game you'll have characters becoming uber-gods in fields like medecine, science, mechanics, different kinds of weapons, unarmed combat, melee combat, hacking and lockpicking, stealth, etc. All by "magic" points which you add to each skill when you go up a level and have absolutely nothing practical to do with the skill themselves. The other unrealistic way to improve stats is by reading a book and blamo you got 10-14 more points in that skill.
You don't learn science by conducting experiments, studying it for years, or any hands on task within the game. You gain points and put them into the science skill and then the game allows additional options related to science during gameplay which were unavailable before reaching a certain point in that skill.
Now this is simple gameplay mechanics, it's not supposed to be a realistic representation of the PC learning and becoming experienced with any given skill. Hell most RPGs have characters becoming experts in ridiculous amounts of time because the way exp is delivered vs ingame time passing is completely unproportional.
My Vault Dweller (In the original Fallout) was an expert in medicine, first aid, small weapons, diplomacy, energy weapons, and was healthy at a few other skills as well as trekking across the Calfornia Wasteland and defeated the Master and destroyed his uber facility almost single handedly (had 3 companions including Dogmeat) in less than 150 days!
My Chosen One (Fallout 2) who was some uneducated dumb tribal managed even more impressive status, fought and defeated entire crime families, took down the Enclave, again almost entirely single handedly save for another dumb tribal, an old merchant, a seasoned fighter and 1 super mutant. And my Chosen One accomplished most of these things in just under 2 years game time from the moment he left Arroyo. Not to mention that the vast majority of the time that was consumed was in travel time between one location to another.
My Lone Wanderer (F3) follows in similar pattern to Chosen One, thanks to there not being a time limit to complete the game such as the original Fallout.
If you take any other RPG you'll see just about the same thing; my peasant farmer in NWN2 became an uber warrior that destroyed a virtually unkillable enemy when entire armies couldn't touch him and then conquered death/mortality itself on death/existence's own plane. All this happened within a ludicruous short span of time of maybe a year or at the most 3 depending how much time you allow for the construction of Crossroad's Keep. This isn't limited to RPGs either; why does a lone Marine manage to defeat the entire legions of hell while every single other counterpart, even more experienced soldiers, get cut to ribbons in games such as Doom? It's all part of video game make believe.
I'm sure you get the point. But fact is that PCs in games are always uber-powered in spite of most being portrayed as coming from humble origins. Just look at it as if fate in that specific video game world destined that PC to overcome all those things and don't pay too much attention to the details like, well, realism.