Only 1 legendary should be allowed per party
If i was balancing the meta (i'd do a better job than Niantic) first thing i would do is only allow 1 legendary per party. Otherwise each pokemon will be trivialized by a legendary.
Zapdos/Raikou trivialized Jolteon and the future Magnezone
Moltres/Entei trivialized Flareon and any fire starter type
Mewtwo trivialized Alakazam/Espeon
Groudon trivialized Rhydon
Kyogre will trivialize Gyarados/Vaporeon
Rayquaza will trivialize Dragonite etc.
So Ultimately Pokemon caught in the wild that you had to get lots of candy for won't matter anymore when you can make teams of 6 legendaries. Getting a Dragonite or Gyarados is like spending weeks waiting to catch a big fish. Getting a Legendary is like buying an even bigger fish from Tesco and showing it off. So there's no value grinding for Wild Pokemon when you can just buy Legendaries and put them all in your party.
So only 1 legendary should be allowed per team. Goodness that would force players to actually think strategically as they're faced with a dilemma which Legendary to pick!
Answers
One per attacking team would have been enough of a restriction. Still allows for the ability to have duplicate legends with different movesets. i.e.: Mewtwos with Focus Blast and Shadow Ball, Groudons with Earthquake and Solar Beam, or if they ever decide to allow placing a legend in a gym then an offensive and defensive moveset.
This is a terrible idea from a business standpoint as it decentivizes whales from tons of money on raid passes and doing tons of legendary raids. I hardly put any money in the game ($20 in past year) and the limited supply of rare candy leads to me having to make hard decisions about which legendaries to power up.
Ofc Niantic might be worried about their income, they put money before all else. People would still do legendaries, for candies, ex points etc. And players would still power up multiple legendaries. Trying a solo a Machamp? Gotta use your Mewtwo. Need firepower against Kyogre? Get that Raikou out!
Eventually you'll get the candies to power up 6 legendaries. (unless you're spending candies on other pokemon) As will everyone else. A meta full of 6 legendaries is going to be rather narrow.
People could say they're very upset that their mighty Rhydon army they raised is now obsolete. Same for Gyarados.
Boo hoo if players are upset, that's all part of gaming when balance tweaks occur no? Some people like that, some don't, They'll all still keep playing.
It should have been done before raids were added for sure.
All my posts are reasonable ;)
I built an amazing Gyarados army in my hardcore playing days, spent too much of my time doing so. Soon everyone will be buying Kygore which takes no effort but they'll be posting them and saying how good they are!! If i was still playing properly that would annoy me a lot.
That's not how a game should function but that's GO for you. Realistically there needs to be a limit on legendary use so there's still a place for hardcore grinding.