Something that bothers me about these skill trees is a few of the perks, specifically the ones such as "full armor on" and "matching set". I must choose these perks before moving further up the skill tree to the next perk, but... My battlemage uses a hood instead of a helmet. Why these perks exist in the first place, I do not understand (they take away from creative thinking and armor combination for better look of a character, by rewarding mindless one-set and ugly helmet using). But, since they do exist, I'd want for them to be located away from the other perks, so you don't have to spend points on useless perks that add nothing to my character.
These perks should at least give their bonus to your character as long as you aren't mixing light-armor and heavy-armor. Make it a pure heavy armor approach perk. (or pure light-armor, in the light-armor skill tree).

But, something I've also been bothered about: The lack of "medium armor". By adding a simple perk into the heavy armor tree, somewhere in the very beginning (right after juggernaut, at 20 heavy armor to choose?) that causes all worn light armor on your character, as long as you have one piece of heavy armor equiped as well, to count their armor-rating after your heavy-armor skill number, instead of the light-armor skill number. Also, taking that perk would make all experience in combat that the light-armor tree would gain, go directly to heavy armor instead. (as long as you have at least one piece of heavy armor equiped).

Thoughts?

The armor trees frustrate me as well, because like you, I typically don't wear a helm or wear a hood instead. As far as mixing in "medium armor" options as you described, I would appreciate a medium armor tree, or even better, combine light and heavy into one tree for armor and just let us pick perks based of what we want to use for armor. That would only work if the trees weren't hierarchal, but that would be how I would want them to do it.

I think this highlights a crucial failing of the perk system in Skyrim. It may not ruin the game, but it is severely prohibitive in how you play. Also, I wish they would stop lumping armor together. I miss the Morrowind system where it was all split up, made mixing and matching a lot of fun.

The answer?

Those are [censored] perks, given meaning solely thanks to the pre-requisite perk system. It's lazy design, finding a way to justify sub-par perks instead of simply creating better ones.

I've only had one character that went full on heavy armor. All the rest have had mixed armors, making most of the armor perks useless. As for helmets, when I have a character that would use one, I just had it hotkeyed so I could put it on with a keystroke when I went out adventuring.

While i wouldn't mind a whole tree for he matching set and full set perks, I too like to use a hood. Essentially i only use 5 perks in the armor tree.

Some of the Tree should have pre-req's, like the ones that increase damage. However, few of the other Perks are really dependent on other Perks, so we should be able to pick them as we want, with some limitations such as Skill Level being the criteria on whether a Perk is availible to us.

As far as Medium Armor, just no.

"Just no", as in, never make medium armor a possible choise for our character's armor, or "just no", as in, making it a specialization within heavy armor is a bad idea, or "just no", as in, making medium armor be light armor + heavy armor things combined isn't the way I'd like it to be, or "just no" as in all of those things?