So I searched around, and I didn't see anything quite like this available. I wish I had the know-how to do it myself, but who know, maybe someone will like it enough to take it up.
I've always thought shouts were too limited. I would like to see a Shout tree added to the skill levels, and the way of using them changed a bit.
What I had in mind was that using a shout starts the timer as normal. However, you may shout again before the timer is finished. if you do, an appropriate amount of magicka or stamina is drained instead, and the timer starts over. The bar drained would depend on the type of shout. It would be pretty intuitive, fire, frost, bend will, etc, would drain magicka, while whirlwind sprint, elemental fury, etc, would drain stamina. The amount drained would correspond to the power of the shout (1,2, or 3 words) and the power of the shout compared to others (shouts with longer CD times would drain more than ones with shorter times).
Finally, you may shout if the corresponding magicka or stamina bar is empty or insufficient, but doing this would drain life instead, potentially killing you.
As far as the skill tree, you would gain experience for using the shouts appropriately. Doing damage to enemies with fire, clearing the skies with Clear Skies, etc. Perks would be increases to damage output, reduction in cool down times and energy drain, and maybe range.
What do you guys think? The game makes a huge deal out of us being Dragonborn, but most times it seems like the ability to shout is an afterthought. I'd like to see shouting become a truly lore friendly yet feasible combat option alongside melee and magic.