Although they don't have an added ability or anything like that (that I know of. Haven't finished the final upgrade yet), anima weapons have that appearance that sets them apart...cosmetically, from other weapons.

And they require a lot of effort and dedication which most casual players just don't have.
So players who want that something special do have the opportunity to get a very nice weapon. And because of the amount of work it takes, it won't be acquired by, I believe, the majority of the community (at least not until it's nerfed and its power becomes obsolete anyway).

But because the anima weapon is not overpowered or have some unique ability that separates players in terms of skill, the game still retains balance.

People can go that extra mile to get that something special without creating a skill rift between players. I have a feeling this is one of the purposes of the anima weapons.