Anyone else annoyed by the way legendary pokemon are treated?

Wouldn't say I'm annoyed - it's a game, and there are bigger issues that us as humans should be getting annoyed about. Like not taxing carbon emissions. But I get your point, and I'd be in favour of a battle party system that limits trainers to one (maybe two) legendaries per party. Given the road we're on now, where we're able to raid as many Legendaries as possible, it's the only wait to limit the influence of Legendaries on the meta and force players to think outside the box for optimal counters.

Wouldn't mind one Legendary per gym on defence either, provided that there are conditions like you must hold a gold medal for that gym.

I started playing only one legendary of each species. I kept the best and transfer all the others. It made more sense to me that way.

Until Mewtwo. SB went legacy and it's the most versatile and viable of all Mewtwo's iterations. So, I have 4 SB Mewtwo in my bag. Plus the best future IV Mewtwo that I catch during the rest of the month.

I would be fine with some sort of limitations, such as allowing only one of each legendary species in your battle party. It would promote diversity and make things more challenging and exciting. People could still use all their multiple Mewtwo, but each one for a different role.

Legendary could be limited for PvP in order to provide more diversification for battle challenge, say one legendary of each type.

Rare Candy is a significant limitation for most players.

I would understand that if they didn't start nerfing legendaries by the classic 9% to all stats. There's absolutely no point on nerfing a legendary if you're limited to using one per battle party for example.

But how would that help Niantic with selling premium passes, their main source of income?

Yes. I always felt you should not be able to own more than 1 of any legendary at a time.

Supposedly the appearance of T5 raids were planned to be extremely limited but due to the shitshow that was Go Fest 2017 they made them as common as other raids as a PR move. How limited depends on what rumor you want to believe; One I've heard said they originally would show up maybe a few times a week in a large city but with extended hatch/raid timers so their appearance would spread via word of mouth. Another one I heard was that *all* legendaries were planned to be EX raids. Both of these ideas are pure speculation as far as I know.

If I could go back and implement Legendary's from the beginning, I'd do this:

1) "Special" Pokémon (Legendary and Legendary) all have the same Stats; you won't catch a "Perfect" or a "0%" because they all have the same stats
2) Each Special is based on a Research Quest
3) The final segment of the Research Quest is that the Special Box is only able to be opened at a Gym you are currently defending, which leads to a personal Raid Battle against that Special Pokémon (with the Raid Boss stats being Tier 1 for Trainers under Level 10, Tier 2 for Trainers level 11-20, and Tier 3 for Trainers level 21+).
4) Special Pokémon cannot be Traded
5) Special Pokémon can be placed in Gyms

Meaning 1 Special Pokémon per Trainer (no army of Mewtwo's like I currently have) and that Pokémon has the Max stats available (so no need to catch another one with better stats).

This would mean changing the Legendary Raids, so I'd rearrange the Raids so that Level 5 would be reserved for "Pseudo-Legendary" Pokémon and other Rare and Powerful Pokémon (like Rhyperior and Mammoswine), and would work like EX Raids but on a larger scale - I would have two days a week (rotating) where Trainers who had won a raid at that gym in the last week would get Passes to one of those raids. It wouldn't be triggered by how many raids were done, or by Badge Level, etc - if you won a raid at that gym in the time frame, you got an Invitation to one of those Raids. If you couldn't make that raid, it sucks - but keep doing raids at that gym and eventually you'll get a pass to a raid you CAN do.