The WoW team want you to feel like your choice is meaningful and that you'll be valued for your choice so they added things like the dungeon perks.
Although I think it's a great idea it comes with some obvious problems. It's great because your covenant is actually meaningful. It means in dungeons you can be to the benefit of your group and in an organised group it won't really matter much but it causes problems for those in LFG. It creates an even more toxic community.
The other issue is that with alliance and horde the player base is already divided on playing WITH each other. Right now it looks like the anima power ups in your covenant zone are covenant specific meaning you can't play with friends. This divides players even more.
It feels like they want people to have a diverse group of covenants in content like m+. They also don't want people to feel like they can't play with friends sometimes and that's what covenants do.
The other issues are with soulbinds etc. If they had given a number of soulbinds that weren't tied to covenants it would have made things easier to balance because there will undoubtedly be turning throughout the expansion and it just makes the swap thing even more clunky
Personally, i believe there are too many systems for Blizz to balance and they need to stop adding power choices that further infuriates players to the point where they'll become apathetic. Just make the covenants cosmetic.
Why add systems that are broken just to fix them a few patches later and say, 'hey look, we listen to our playerbase.'