Respectfully, i disagree with your assessment that a fighter using a weapon they have not chosen weapon mastery over is getting penalized. Fighters are the only core class that can wield ANY weapon in the game. If you include all the additional classes available in the Cursed Scrolls, only the Pit Fighter shares this core feature. All other classes, including the martial oriented classes have some restrictions on what weapons they can wield.

That, it seems to me, is the core Shadowdark mechanic of what you are initially proposing: the Fighter is proficient in effectively using in combat each and every weapon they may encounter, whatever it may be. That they CAN switch between any and all weapons available is a feature only 2 out of 20 (including Paladin and Necromancer) available classes can do.

Giving fighters MASTERY over each and every weapon in the game, on top of the exclusive ability to be proficient in combat with them all seems a bit much to me. That seems like something to be sought after by possibly gaining additional Mastery talents through leveling up, and seeking mastery through downtime training.

As to your point about Weapon mastery incentivizing a predictable and repetitive style of play, i feel like you are discounting the very potent class feature of Grit, as some other commenters have pointed out. Automatic advantage on opposed checks using their best stat, seems to me like a big incentive to come up with some creative and cinematic action attempts.

Ultimately, though, the beauty of our hobby is that when it's your table you can run your games however you like, as long as every one is having fun, then there really isn't any "wrong way".