Personally, I love two-handed weapons guys, and I play them with Offense and Utility tree stuff and usually nothing from the Defense tree. Yes, really.
You’re not carrying a big weapon so you can take hits. That’s what shields and nimble fighters are for. You carry a big two-handed weapon because something needs to die and it needs to die NOW.
Key to any offense-oriented two-handed build is having a hornblower in the back to assist, especially if Perfect Focus is going to be a part of your setup. You might even use the offense tree perk that gives you extra AP on murdering someone in conjunction. That can give a guy using a polearm a lot of extra attacks, or a guy using a two-handed sword one or two extra swings after an initial AoE strike (depending on how much fatigue they have and if they use Perfect Focus).
You probably want Brawny from the Utility tree. It lets you wear the biggest, bulkiest armor in the game, meaning really good defense – and since a patch that I don’t recall, this applies to helmets too. Wear big stuff and add that heavy armor to your damage with the Full Force perk.
The Full Force perk seems to be REALLY good on weapons with low base damage but high armor effectiveness, such as the two-handed hammer. Keep that in mind when picking weapon loadouts: try to have a weapon that’s good vs. HP, a weapon that’s good vs. armor, and a weapon that’s got reach, always. Some weapons will fit two of these criteria, such as the billhook being good vs. armor while having reach, or the longaxe being good vs. HP with reach… or the two-handed orcish axe (the Mansplitter) which just makes a mockery of flesh and armor alike at the cost of ALL YOUR FATIGUE. Your mileage may vary with that one.
There are five stats you should level with this setup, taken whenever the dice rolls heavily favor one or the other: Melee Attack, Fatigue, Melee Defense, Hit Points, and Ranged Attack. You want Ranged Attack because crossbows are magnificent backup weapons for your two-handed warriors.
Sellswords are pretty good choices for this role, since they start with bonuses in both offensive stats. Hedge Knights, Wildmen, and Farmers can do very well in this role as well, and others might fit if they get good traits. If your character you’ve chosen has high enough fatigue (such as a Strong Athletic Wildman), you might not take Brawny at all, and instead get one of the perks from the Defense tree (+HP or -armor damage taken), or perhaps take Fearsome since any amount of HP damage from an AoE can then trigger morale breaks on the enemy.
A general note is that a two-handed warrior is NOT an all-rounder. Two-handed warriors are specialists. Treat them as such. Make sure your defense-oriented characters have Rotation so you can pull your two-handed dudes out of a fight if you must; they can soak damage, but they can’t dodge or block it, so once their armor is almost gone they’re definitely going to need help.
When fighting orc warriors, something to remember is that a Nimble fighter or shield fighter (whose enemies don’t have axes) can hold the line practically forever, allowing your two-handed warriors to stab at afar with polearms. HOWEVER, you don’t want anyone to be standing directly behind the defensive warriors, since if they’re adjacent an orcish warrior can simply shove them aside and then swing at the polearm fighters. Instead, have your pikemen/billmen keep a 1 tile distance away from both the orcs and the defender. They’re unlikely to try to break away from the defender if the defender has a high attack value, and they’re unlikely to shove him around if there’s nobody they can reach by shoving him. It’s a nice way of tangling orcs up if you have someone with incredible defense.
(Note: the above piece on fighting orcs changes if your defenders have Indomitable.)
Finally, one thing to remember is that you should always carry a ranged weapon (since you have two free hands anyway) via bags and belts. A crossbow or bow will give your heavily injured two-handed warriors an option when they back up from the fight. Furthermore, they should get plenty of shots thanks to Perfect Focus (again, a must-have if you bring a hornblower). And… remember that, presently, two-handed builds aren’t going to be the best mostly because there are a few specific builds that are simply rather dominant. But they do have their place, and they’re incredibly fun to play. Their damage is incredible, and they love wearing the best armor you can find. I like ’em.
As an aside, Berserk is something I definitely like for two-handers, but I’m personally a fan of Perfect Focus over Killing Frenzy. This is largely because you can’t always make sure the two-hander guy secures kills, and sometimes it may just be more economical to let someone else take it because their weapon deals less damage and there’s a fresh orc standing to that wounded enemy’s left. But both the top-tier offense tree perks have huge value to a two-handed weapons guy, and I imagine Killing Frenzy is amazing with a two-handed hammer, especially with the right character traits.
One thing I’ll note is I LOVE finding characters with massive starting fatigue pools (again, Wildman with Strong and Athletic, or Hedge Knight with similar) because I can give them much better defenses than usual. I once had a Wildman with Strong who I didn’t give Brawny OR Pathfinder to, but instead gave the HP-boosting AND armor damage taken reducing perks from the defense tree. This made for a massive increase in survivability, though the guy moved like a turtle through swamps.
There’s a lot of really good Tier 2 offense tree perks, to be honest. Berserk and Full Force are just two of ’em. I could see the merit (if you wanted more oomph) in taking more Tier 2 offense perks in lieu of 1-2 Utility tree perks. Fast Adaption is good if you really need more Melee Attack; Close Combat Archer for when you want to shoot a guy with a crossbow, swap to your two-handed weapon, and swing at his face. (Again: thank you, Quick Hands + Bags and Belts.) Bullseye is good for just being able to play backup sniper, and Debilitate could be useful when fighting, say, an orcish warlord carrying a greataxe. All of this stuff is really, really juicy, and it’s worth experimenting with.
Tier 1 perks for a two-handed weapons guy can be tough to choose. If you plan on using greataxes or the two-handed hammer, I’d definitely consider Crusher a good choice. Bloody Harvest and Sundering Strikes are both really good. Head Hunter could be good for Brutes, and Executioner is a good second pick after Sundering Strikes if you don’t plan on smashing shields. Really, there’s just a lot of good choices here, and the only one I’d say is a poor one for a two-handed guy is Push the Advantage – unless you’ve got a lot of macemen around and you’re specifically not fighting orcs.
And again, your Tier 3 perks are both very good. But they operate very differently on the field: one gets extra damage for a brief time after each kill and doesn’t have fatigue issues, but the other makes multiple extra attacks and has more tactical mobility (move 2 tiles > perfect focus > stab with polearm) at the expense of lots and lots of fatigue. The other characters in your mercenary band are critical in deciding which to use, and if you decide to use the Perfect Focus perk, you need to keep your two-handed warrior within range of Rally the Troops.
Lastly… One thing comes to mind that might be interesting to try: a two-handed Warrior with Footwork instead of Brawny. Again, you’d want high fatigue if you do this, but having the capability to pull out from bad situations with Footwork and then stab at your opponents via polearms could be incredibly useful. It’s a curious thought, but it might work with the right builds.