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One more idea before it slips I think you should make rainbow dragon alot more special and earned by only allowing us to enter only by catching all seven crystal beast and you can only battle rainbow dragon with 6 out of the 7 also i think rainbow dragon should have a regular and an ultra form...
As for neos as a work around I'd have neos be able to Evo when a certain neo specian is in front it after it lvls up then have those Evo again with each stone eg aqua neos water stone into storm neos
Love this romhack but some of the evolution could be better like red eyes should evo into red eyes darkness dragon whilst having metal dragon be an option via metal coat. Dark magician should've Evo into dark eradicater because age wise it comes before dark sage or simply have it be an option...