Fighter Weapon Mastery.
As written, Weapon Mastery applies to a single weapon at character creation, with the chance of applying it to additional weapons as the character levels up. I feel that there's a case to be made that it makes sense for it to be changed to apply to ALL weapons from the start.
The specialisation encourages the player to seek to use the favoured weapons in as many situations as possible, even when it makes sense to try a different tactic. It becomes a case of viewing every problem as a nail. The fighter crawling in the narrow tunnel will probably favour his long sword over a small thrusting weapon, even if he's penalised for so doing. None of the other core classes has this issue. A priest or wizard can simply cast the spell most suitable to the circumstances. The thief likewise can apply the relevant skill to a problem.
You may regard this as a feature rather than a problem, but I don't see the upside to it. You can argue that it's the players choice whether they want to suffer the penalty of using their favoured weapon in sub-optimal circumstances, or suffer the penalty of using a more appropriate weapon without the benefit of Mastery. But is seems that the fighter is being penalised more than, say, the wizard, who puts down his staff and draws his dagger before crawling into the tunnel.
It does result in the fighter being front-loaded, in that all that happens as they level up is that their numbers go up. But this is already the case for the thief.
I think in the end that Weapon Mastery in a single weapon serves to disincentivise the player from trying other options - not just using other weapons but also attempting other kinds of actions in combat. Fighter's often fall into a routine in combat of attacking with their favoured weapon over and over again. I would prefer - if they're going to simply attack again and again with one weapon - that they chose that option from a range of equally good options, rather than that they chose that option because they would be penalised if they didn't.
BTW, this is written from a GM's perspective.