I think it is a combination of the mc’s weak health and stamina, they were tortured the most on top of already being the youngest and weakest to start with and their incomplete education, due to the mc being stupidly young, back as a ward of the court in Salantira. Which apparently meant that unlike Eli and presumably sister too they never got around to having the master of arms instruct the mc in weapon handling before sister’s little coup and Eli’s first death.
Anyway it seems the mc did miss out on the both the more advanced magic and weapons training for Salantiran nobles back in the day. 
They also seem to have lacked the kind of freedom of movement that sister and Eli seemed to have enjoyed.
Then back in Leaf’s end the mc was weak, penniless and recovering and needing to earn their keep.
Why the mc never took advantage of the opportunity to potentially learn something and acquire a weapon during the White Fang days is beyond me, Saine or Leo could probably have taught the mc a thing or two then. 
No weapons training and the mc’s shit health seem to be the main culprits for that and in the case of mine it is presumably too late now, unless primitive guns already exist as the cripple, in constant pain, he is now is never going to learn fancy footwork and a bow, while good for physique and upper body strength is indeed less of an advantage over a ranged spell.
It’s not, not really it needs months of recovery time after every use, unless Eli tortures the mc under the guise of “healing” as pain killing is either not something his phantasma knows how to do or one of the phantasma abilities that no one knows how to use anymore due to the old Arcadians being paranoid assholes who were terminally stupid.
I mean technically my mc’s main torturer, Nyx, could be actually useful as it is implied she has a whole other side of healing/resurrection/vivimancy that no one that we know of in the mc’s era knows how to access. Maybe she could even heal the limp by regenerating the bones or something, which is something even Eli’s pure healing phantasma either cannot do or is also an ability Eli cannot access due to that knowledge being lost somewhere in the terminal stupidity of old Arcadia.
That could actually make her earn her keep where my mc is concerned, the other three total freebooters would still need to sod the fuck off though! 
Your mc’s main tormentor is the enchantment one, right? Which is even more frustrating because it is implied by Thalia that one should be able to do a super disenchantment/dispel magic that is likely powerful enough to get rid of the stupid arcane collar in a second, only you don’t get to access that one either.
Actually you do, as the mc cannot even access it quickly enough to prevent Thalia’s little tricks. So in the hands of the mc it is not powerful or even useful enough to do anything against Thalia.
The mc can threaten to use the Earthworm but it doesn’t actually lead to anything meaningful.
No, it does not, using it is still torture for the mc, that requires more torture from Eli and Thalia to “heal and recover” from those practice sessions.
Is it less torture than using the only other phantasma the mc can use? Maybe, it is still very painful though and it actually seems less powerful than Nyx too, at least to me.
Instead it mentions Eli’s healing sessions to recover from using it being painful enough to make the mc wish they were dead again, on occasion.
This seems to be closest to the truth. Although even without the other parasites it still wouldn’t work completely fine either as the text explicitly mentions the mc being still slightly out of sync with the Earthworm thing. The self-inflicted torture still seems to be present though and that presumably does come from the fact it needs to draw its power from the same blood/mana that is already invested with four other parasites.
It would probably have been mostly fine, mostly if the Earthworm thing really had been the only parasite the mc had to worry about, but it is not as there is still one other semi useless and three completely and totally useless ones to contend with.
Of course in the case of my mc the Earthworm was yet another parasite that was basically forced upon him, which doesn’t make him particularly favourably inclined towards it to begin with.
Even if that is true, the mc seems fated to meet more of the elites than the average or weak ones. I am almost certain Thalia is a 10 even in normal magic and Yu a 9. Sister may also have been a 9 in normal magic and Eli is probably roughly comparable to the mc. Although this is mostly speculation based on Yu’s family being made up of extremely strong mages, including the Saintess herself and in Thalia and Sister’s case around the Arcane collar.
Unless they really are re-using the one Thaubal put on the mc, the Arcane collar trick may be one of the things you’d need to have at least a 9 in magic power to put on (or take off) somebody by conventional means.
Of course Thaubal himself must also have been at least a 9 in normal magic in that case.
Which comparatively makes the mc relatively weak, even if that is not true in absolute terms it may well be the case compared to many of the mc’s book 2 enemies and allies.
