The rainbow has always been a major element of the MLP story line. In G1, the Rainbow of Light was the ultimate magic that the ponies turned to when they were attacked by Tirek. In G4, when the Mane Six utilize the Elements of Harmony to defeat Nightmare Moon, there is a definite throwback to the Rainbow of Light. Later, the Mane Six harness the power of the rainbow itself. At various times, the rainbow has featured prominently in MLP packaging and promotion.
The original Rainbow Ponies were some of my favourites when I was a kid, especially Windy and Moonstone (unicorns being my third great weakness). I envisioned them living among the clouds and the rainbow above Dream Valley, visiting with the other ponies, but a separate species like the Sea Ponies or Flutter Ponies.
The Rainbow Power era of G4 is when I began my Twilight Sparkle army, basically because Hasbro made too many pretty rainbow variations and I couldn't decide which one to keep. At least I managed not to get rainbow variations of all the Mane Six.
The original Rainbow Ponies were inducted into the My Little Pony Hall of Fame in 2014, and rightly so.
Elf