Gem-Knight =/= Hero Gate. Gems fuse normally with GKF. Run 2 Tourmaline, Sapphire and Garnet. Run also triple Turtle and Armadillo. One or two Obsidians, Alexandrites and Ambers will fit the theme. To finish the deck place Thunder(3 Thunder Dragon/maybe a Rai-Oh), Pyro (3 Volcanic Shell/maybe a Gaia Soul) and maybe Aqua monsters(namely Treeborn Frog and Mobius). Citrine, Aquamarine, Zirconia and Prism Aura wanna be your main fusion monsters. Aura pops, Aquamarine bounces, Citrine attacks, Zirconia finish. Master Dia is also viable, and run 1 copy of each other Gem-Knight fusion monster(2 Amethys if running Treeborn). Don't run s/t other than staple and FF/GKF.
About Dark Gaia, try use cards to discard/send monsters like Caius to grave(treeborn fits well here) and then use Calling, Return from DD, Release from Stone to cycle from RFG Zone to field to grave to RFG Zone, like Psychics.
Thanks duellogs! xD