I think i'm just totally confused by the character build system right now. It's not traditional by any means. It's almost like you have to think backwards. If you are a mage you don't want to put points into magic and just concentrate on that skill tree. If you are a rogue you want to bump the other stats and ignore stamina and concentrate on the stealth tree. Am I correct?
Well, the game doesn't have classes to begin with.
Think for a moment, what is a rogue? It's a playstyle and a couple of skills, specifically
One-Handed Weapons
Light Armor (However, where it gets sorta funny is that the reason you use light armor is because it makes less noise, making sneaking possible, but Sneaking has a pe that removes the noise from armor!)
Sneak
Archery
Lockpicking (DO NOT EVER PUT POINTS INTO THIS, it's trivial to pick locks without any skill points)
None of these skills are reliant on stamina. Stamina is used for Power Attacks (which you rarely make in sequence, and the game is overloaded with stamina potions/food), running and using the zoom perk on the bow. They're all cute, but none of them are important.