Problem is that current system reward using strict specialised build and there is problem with plenty of little worth perks or perks overlapping in one tree. Not even mention some perks that are only worthwhile for specific builds.
Although it would be nice to have some sort of Random perk tree for all soldiers Option on the start of the game.
Lets look at Utility tree(the bigger offender).
First it contain 2 best 3rd Tier perks as they are have company range and are plainly speaking necessary for a good company.
Then you have almost zero choice in 1st tier perks. Th Holy Trinity of Utility(Quick hands, Bags Belts and Pathfinder) is must when rest perks can not even compete.
2nd Tier have plenty of Fatigue oriented skills but for example Quick hands and Bags and Belts make Weaponmaster obsolete(even if its one of my favourite) as you can easily carry spare weapons for no fatigue cost. Battle flow is rather useful perk but only for characters who do killing and for full utility or utility-defensive hybrids it present little worth. Then there is Captain that is only for resolve builds(Hornblower/sergeants) and Brawny that is no brainier as it offer great Fatigue boost on any heavy armoured soldier. Fearsome is great perk to have but it really shine when you employ its in mass on many characters with specific weapons(hammers, xbows). Footwork can be useful sometimes but its costly and offer little benefits compared to other perks.
In the end its really clear path of perks to take.
1st tier Trinity of Utility
2nd tier Captain for resolve build, Brawny for all, Battle flow/weaponmaster for PF builds, Fearsome for hybrids and line soldiers
3rd tier one inspiring presence as its boost whole company, two rally the troops for keeping them fighting
Offensive tree offer rather limited choices
1st tier perks are again no brainier, Sundering strike is best, executioner can be useful, Crusher is decent for axe user, then its Bloody harvest for AoE weapons and that its all. No really a choice
2nd tiers is either Berserk and Fullforce for melee or berserk and CCA/Bullseye for ranged
3rd tier is either PF for PF build or Killing frenzy for rest
Defence tree offer most options especially on lower tiers
1st tier offer plenty of choices(although 2 perks are only for shield users and dodge rely on secondary attribute)
2nd tier have some interesting options but Nimble for Nimble builds and Hold out for rest stay out from the rest
3rd tier return the favour for nimble build, Indomitable for rest
Overall I would say that current perk system is very rigid and limited. It lack flexibility and interesting choices to make. You can say that something is wrong when you can name specific builds after one perk.