Yes, "Future Fusion" can be used for "Rainbow Neos" by sending an "Elemental Hero Neos" and a "Rainbow Dragon" or "Dark Rainbow Dragon" from your deck to the Graveyard.
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You use any appropriate Fusion Summon card (ie Polymerization) while you have Elemental HERO Neos and any 'Ultimate Crystal' monster such as Rainbow Dragon, either in hand or on the field.
Fusion Monsters that are summoned without using Polymerization (and similar) cannot be summoned via Future Fusion, meaning you can't select them for Future Fusion in the first place. Other monsters that this applies to are Gladiator Beast Heraklinos, Armityle the Chaos Phantom, and the Neos fusions such as Elemental HERO Dark Neos.
you run three elemental hero neos alius and cards that special summon normal monsters from the graveyard like skyscraper2 hero city and hero blast to grab neos alius or neos from the grave and use alius special effect to be treated as neos. then use three common souls in your deck. also add copy's of neo spacians like glow moss, air hummies. grand moles are limited. so run that with "ribbon of rebirth". to bring moles back to the hand along with opponents monsters. use three compulsory evacuation device and torrential tribute. Then you need to use those common souls to grab those neo spacians from your hand onto the field and there you go. CONTACT FUSION!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!elemental hero grand neos
No, you cannot use Fusion Substitute Monsters for "Future Fusion". You can, however, use Fusion Substitute Monsters for "Chain Material" as long as those Fusion Substitute Monsters exist on your field or hand. The reason Fusion Substitute Monsters cannot be used from your deck is because they have no substitute ability while in the deck and thus cannot be used as replacements for other Fusion Material Monsters.
No, Elemental Hero Dark Gaia cannot be special summoned, except by the effect of 'Dark Fusion'. You cannot use any other special summon methods (like Monster Reborn), or even other fusion summon methods (Polymerization, Re-Fusion, Future Fusion).