Here is part II of my mini-series of thoughts on Weapon Master and its consequences. You may or may not like these consequences. I'm really just observing what I see and what I think the results of the advantage being freely available is on a game.
How do you make sure monsters are a threat to Weapon Master PCs?
The simple answer is, "Just use more monsters!" or "Just use stronger monsters!"
That's fine, and it works to a degree.
The monsters must be designed with dealing with WM in mind or they're going to provide a less-than-expected challenge. Rewards are less appropriate to the challenge if they're easier because you're getting more, higher-damage attacks against them and fending off more attacks with less penalties. Or monsters are designed with an eye to WM foes, and are thus more dangerous themselves. That balances them better against the WMs.
But it further leaves the have-not PCs in a hole. They're facing increased numbers of foes, yet effectively attack less often than their WM-having buddies and defend against multiple attacks less well than they do, as well. Or they they're facing foes designed to absorb multiple defense penalties (or get around them by having a high Dodge), the DR to absorb an additional +4 to +6 to even +8 damage expected from a WM PC, or the ability to saturate defenses to deal with the WM's ability to defend multiple times more effectively.
Essentially those are decisions I make when I'm designing a "boss" monster for DF. The assumption is the monster must have the DR to deal with very-high-damage threats, because the "low" damage PCs can inflict 10-15 points of raw damage. The monster must be able to deal with 2-4 attacks per PC per second; out of each block of attacks one is likely to be a high-skill Feint. The monster must be able to deal with high defenses without needing to saturate them to do so, because defenses will, at worst, cascade down at a -2 and likely will do so from two pools (dual weapon or weapon and shield) or be at -1 (fencing weapon or two-handed sword) or both. All of this is without Great Haste more than doubling the threat of the PCs, as the first turn will be an All-Out Attack.
They may or may not need enough HP and damage-reducing advantages to survive all of this anyway; Regeneration is nice but unless it's at least 10 HP/second it'll get smothered. A worthy foe merely needs to be able to this against one PC; a boss against multiple. If they can't hold up more than 1-3 seconds of this, they're really just fodder by another name. And the ones who can hang with WMs for a while like this can generally ignore non-WMs unless they get a lucky break or jump in between WM character turns.
Much of this exists without WM, but it's all to a higher degree just with the addition of a 20-to-45 point advantage on a PC. WM effectively attacks as an attack-and-damage multiplier on a PC and thus makes them more of a threat to that worthy or boss foe, and may reduce worthy to fodder and bosses to worthy. If that boss was meant to take on 5-6 PCs and now faces 5-6 but can only hang with 1-2 WMs, the reward it provides just won't make much sense. Any loot will probably be turned into more power, contributing to the lopsided nature of the encounter later.
There are consequences to decisions elsewhere in the game system. This is one of them. Much like how magic system choice dramatically affects the threat of monsters, so does WM. Magic might make ranged foes helpless (Missile Shield) or provide the only way to fight them (ghosts, say), but either way it's a change. I'm arguing here that Weapon Master is such a change, too, since it makes a category of PCs (the haves) able to more effectively deal with monsters as foes than a non-WM would be.
So monsters are affected by WM, too, and by monsters I mean the GM's adventure design. It's harder to appropriately challenge a WM PC without making non-WM PCs basically irrelevant.