Yet another suggestion, but I think this solution has the right balance in it to make everyone happy (and it builds off of the existing 'Book' system).

Why not just roll in the Atma acquisitions with book purchases?

Two book sets: one for Atma and one for Animus.

Atma upgrade books would require 500 Mythology Tomes to buy and after you complete a book, then you get an Atma. That would make it so an Atma weapon would cost 6000 tomes (about half of what an Animus weapon would cost) which is very obtainable casually. After 12 books you can upgrade to the Atma weapon (ilvl100 with a Stat boost). Once you complete the Atma books, you unlock the Animus books.

Obtaining the Animus would still be as it is now... but instead you get 10 ilvl bump to ilvl110 to put it on par with the Weathered weapons. Or even a 5 ilvl bump if you think it would make the weathered weapons pointless.

I think something like this would be pretty balanced and make everyone happy.