I am digging the game, but i thought of something that makes sense to the perk system. Maybe to allow you to specialize after you have maxed out your main perks, you could allow the player to get a passive bonus of 1+ to any of the stats (agility, strength, dexterity, constitution, intelligence). This would be like the poison resistance but more tailored to all characters. It would be much easier to implement as it was in previous versions.
So here's how it might work. There are no restrictions on stats so you can do strength, dex whatever at any level. It will give that character a chance to specialize further as +1 is with each level up to level 3. So you get +1 t the first level, +2 the second lvl and +3, the 3rd level.
If you think about it, it might not be a bad idea as the game is already rockin. This will not only be simpler to implement but it will allow you to also have something to specialize in when high lvl and maxed out everything.