- Pole weapon proficiency
- Two-handed sword proficiency
- Axe proficiency (which includes both one-handed and two handed ones)
- I forgot the rest, but you probably know the list of proficiencies.
Now, here lies the problem.
Let's say I choose to use a two-handed weapon with 30 AC. With one weapon proficiency skill, it gives 30% increase in weapon's AC, which means AC +9.You also gain 30% increase in weapon's BC, which is mostly useless because you don't get much BC, unless you use weapons like Xul'viir, Defender's claymore, Superior defender's claymore, Spike gloves (maybe? I haven't tried a build with this weapon). Those are weapons with more than +10 BC.
The last advantage from weapon proficiency skill is 10% increase of weapon's critical skill. Now, this is useful if your weapon comes with critical skill and critical multiplier. However, if you do a heavy armor built or non-critical built, most likely you don't care about critical hits.
Thus, the only useful gain is the 30% increase in AC, which gives AC +9 for a weapon with 30 AC. If the extra BC and critical are useless for the built, then this weapon proficiency skill is inferior compare to Weapon Accuracy skill, which gives AC +12 regardless of what weapon you use! In order to get more than AC +12, your weapon will need to come with 40 AC to begin with, which none of the weapons do (again, Blackwater weapons are debatable due to Blackwater misery effect). You can only achieve this by making a dual-wielding built which wields the same weapon type (I have a dual swords wielding heavy armor, which is awesome) because two weapons definitely gives you plenty of AC with two swords or two daggers (two of the most common weapons in game).
So, what to do with a built, let's say, polearm with heavy armor? For pragmatic reason, instead of investing 2 skill points into Polearm weapon proficiency, it's more advantageous to invest them in 2 level of Weapon Accuracy skill for maximum gain of AC. This makes the built sort of able to use various different two-handed weapons (I know, the 1 skill free from the dude I saved in Charwood still give some extra AC). On the other hand, heavy armor build is already at disadvantage because you need to invest 3 skills into heavy armor proficiency to max it as oppose to 2 skills to max light armor or no armor proficiency.
You may argue, since he is a two-handed weapon user, why not invest in Fighting style: Two-handed weapon for additional damage, thus you can use your level bonuses on AC. Well, it adds little damages for most two-handed weapons, unless it is Wraith's massive claymore, Xul'viir -- you should realize by now how powerful Xul'viir is, Steel claymore, Skullcrusher, Maul -- who use this anyway, or Gutsplitter.
So, let's hear out how others deal with this. Thanks for reading this lengthy post! As my toddler says, you deserve two thumbs up!

PS: Why I do polearm with heavy armor? Because I love Zhao Yun (or Zhao Zilong) from Romance of the Three Kingdom, one of the best spear-wielder in the story. He is always depicted wearing what may be considered as heavy armor.
PSS: I almost build a polearm wielder with cloth armor to imitate Guan Yu, but in this game, this will be a very challanging built to play with.