Nice sharkies!
I did some brainstorming for unit ideas for each civ, we don't have to use all of these, but I thought it might spark some inspiration. A few of these were mentioned earlier in this thread.
Hyrule: Castle Guard, Hylian Knight, Sage, Sheikah Ninja, Bomb Cannon
Termina: Guardsmen
Gorons: Rock Chucker, Bomb Thrower, Goron Clubman, Goron Puncher, Goron Hammerer, Dodongo Rider, Rock Golem
Zora: ???
Deku: Deku Scrub, Deku Shaman, Deku Stick Wielder, Deku Flower Flyer
Kokiri: Kokiri Slingshotter, Deku Nut Cannon, Kokiri Stonethrower, Kokiri w/Wooden Sword or Deku Stick, Skull Kid
Gerudo: Gerudo Assassin, Swordmistress, Pirate, Spearmaiden, Thief, Priestess
Ikana: Stalchild, Ikana Swordmaster
Evil Forces: Too many to mention (Moblins, Lizalfos, Stalfos, and such)
I had trouble coming up with something creative for the Zora. But, it shouldn't be hard to find graphics for most of these units, except for maybe the Goron, Deku, and Zora units as I don't recall seeing anything that looked like them in the unit graphics forum.
I agree each civ or culture group should have a different tech tree. I think the tech tree should also have a line of techs in each era that mark important events that happened in LoZ history along with the typical technologies. For scenarios, you have techs that gradually upgrade Link into a stonger unit giving him more abilities and bonuses kinda like the Shoguns in the Sengoku conquest. There also can be different techs that represent items you get in the games which in turn reveal new resources on the map to further your quest.
@Odin - Here's a post I made like 2 years ago about a windwaker scenario I was thinking about doing. Ironically, it was in a thread where you were requesting a Zora LH.
When Windwaker first came out, I had actually considered making it into a Civ3 mod, but C3C wasn't out at the time and it couldn't be done. Now that C3C is out and I think it through right now, Windwaker could very well be easier to make into a mod. Especially by using Reverse Capture the Flag to complete certain tasks.
Substituting the SS parts with the 8 Triforce shards could be made to simulate the Spaceship Victory. Each Triforce shard could require a different resource called Triforce Chart 1-8. In order to see those resources, you would need a tech called "Incredible Chart".