1. Malakim - Graphics, Varn Gossam (Adaptive), works well with religions, Deserts, the theme of Malakim is really great if I play them. If the AI plays them, I hate'em.
2. Clan - very cool design. Units like lizardmen, goblin, ogres, are so flavourful. you can play as barbarian, but with a proper Civ.
3. Luchuirp - The Golem Approach with that many Improvements is something completely different.
Others: Elohim, Lanun, Mercurian, Infernal, Balseraph, Svartalfar, Shaeim have also very good themes.
Khazad, Amurites and Grigori, are too weak in my opinion, that makes them a bit less preferred to me. Even though they are fun to play. But somehow they could use more Dwarven units or Dwarven mines, Spellcasters or special buildings, Heroes or units like the Luonnatar healer respectively.