Him Not Being Able To Fight Is Literally A Whole Subplot In My Opinion. Early On In Tfc He Actually Says

him not being able to fight is literally a whole subplot in my opinion. early on in tfc he actually says how he is an instigator through and through and can only start fights, not finish them, assumedly because of his smart mouth

“Neil was much better at instigating fights than winning them, but it'd be worth losing if he could just put a fist through Kevin's face once. Starting a fight was too out of character for who he portrayed "Neil" to be, though.” - tfc, chapter five

he realizes that he cannot fight, that he could throw a punch or two but would get his ass beat cause that’s not his strong suit. with weapons it could be a different story but like OP said, his training was when he was very young and mary took him before he moved on to cutting up the human body (it actually wasn’t EC, it’s in tkm which is cool)

“He didn't say he'd used knives before; one couldn't grow up a Wesninski without having a blade pushed into his hand. Nathan didn't have the time or patience to teach his son but he'd put two of his people to the task. Luckily Neil left home before he progressed past cutting up hunks of dead animals.” - tkm, chapter three

we can guess that on the run, he had to put his limited fighting skills into action to survive and that he might be a bit better if he had a gun or a knife but he is not close to renee’s level and that’s okay. he doesn’t want to be. he even admits that he doesn’t want to learn how to fight with knives because it reminds him too much of his father.

"So those knives [Andrew] brings everywhere are yours?" "Were mine," Renee said. "He was right; I don't need them anymore. If you need them, he will give them to you, and I will teach you how to use them." She wasn't smiling anymore. Neil studied her calm expression and knew she meant it. She'd put her faith in mankind and her Christian piety on hold and show him how to cut a man open throat to groin if he asked her to. […] "Thank you," Neil said, "but no. I don't want to be like—him." - tkm, chapter three

and him not being good with his fists is important because he feels a bit helpless after drake happens and goes to matt to ask him for help. because matt knows how to fight because of his mother and neil is aware of that, aware of his shortcomings, and asks for lessons

“That night he asked Matt to teach him how to fight. Matt looked surprised by the request but agreed, and they spent the rest of the evening figuring out when they could possibly meet up for lessons. […] Matt promised to get Neil a pair of gloves the next time he went out.” -trk, chapter fourteen

neil not being able to fight is important because it goes hand in hand with him being a runner. he knows how to start fights and how to run away from them. we can even assume he knows how to fight just enough to find an opening to run. but throughout the trilogy he is learning how to stand his ground and not run at the first hint of danger. learning to lean on others and how to fight is part of that journey meaning he has to be bad at it at first. and i don’t believe he ever gets great at it. because he doesn’t want to pick up a knife and while he learns how to fight from matt (which is phenomenal, i love their friendship so much) part of point of the books is neil healing and not needing to fight anymore. after riko dies and after baltimore, neil has less reason to know how to fight than before and i think he doesn’t put his full effort in mastering it. i believe that he learns how to stand his own in a fight because he wants to have the safety that comes with it but knows that he has andrew to lean on now should he need him

i keep seeing people say neil is canonically better at fighting than andrew??? genuinely confused as to where this is coming from outside of fanon...like genuinely why do people think he can beat andrew or even renee in a fight? neil is not physically intimidating like andrew. he is not capable of the same physical violence (maybe if u give him a gun). and yeah i see people point to his upbringing with nathan and MAYBE im cheating bcus im pretty sure this was only mentioned in the EC but his training never moved past dead animals. mary literally took him and ran before they could move to training him on live ones, and i think that's evidence that he wouldn't be some insanely crazy good knife fighter (also the fact all of this occured before he turned 10).

and call me crazy but there's No Evidence that Mary taught him Any physical fighting while they were on the run during those 8 years. in fact i think there's more subtextual evidence for her refusing to teach him both so that 1) he'd remain dependent on her and 2) so there was no chance he could become like nathan. like did we forget that his whole thing is getting his ass beat. over n over again. this is, i would argue, one of his most character defining traits. the foxes' battered wife in the wise words of one david wymack. mr "i start fights and let andrew finish them" josten.