Well, with Mothra you could go two routes, one where the serious tone is intact, while the other one is more of a Pacific Rim/Marvel tone.
Serious Tone:
1. Mothra is from the species of a unique prehistoric lepidoptera insect. (Before anyone says no, hey, Toho did a prehistoric Mothra before in Rebirth of Mothra 3:
A species that is fairly non-aggressive and prefers a stable environment to live in. And will only engage when that stability in their territory is threaten. (Kinda like when someone stirs a bee hive, hornet's nest, etc. When someone does that, you're basically messing with their stability which causes them to get defensive. This will at least explain Mothra's peaceful nature trait nicely well without going into the whole protector of the earth deal and fairies.)
Mothra's kind could have lived probably around the same time that Godzilla originally did before his reawakening in GODZILLA. Just to give her some backbone on her origin. To which brings me to my next point.
Prehistoric insects were massive back then during the age of the dinosaurs due to the earth's intense atmosphere. So with that, you could use that to explain Mothra's massive size with a little tweaking of imagination.
Route one is for a more, natural Mothra, like Showa Mothra or GMK Mothra. By natural I mean a Mothra without all the lasers and reflective scales, etc. (Heisei and Tokyo SOS-Final Wars)
Non-Serious Tone:
2. If you want to introduce Mothra with all the fixings, then you'd probably have to get rid of the dark tone and go for a more Pacific Rim/Marvel movie tone.
I think we can work around the fairies/cosmos a bit, but it'll be difficult to a slight extent since Mothra and her fairies are like two peas in a pod mostly.
Only GMK manged to work without them, then again Mothra was a mystic beast/Guardian of the land of Japan. And their origin was clarified rather quickly without fairies due to..Well, fans should already know with the spirit of the old man and all.
