I think much more people than me don't like when rayquaza simply floats above hills behind your house, when zapdos needs much boss hunting in order to get this stupid orb, and mining all this thunder shards. Plus charging... And finding a shrine... Some legendaries is powerful but too easy to get. I have a few ideas on certain legends to fix it:
In order of getting Gro/Ky you must first find blue/red orb. (You know fishing in oceans and desert lavas). Next you must find one of Caves Of Origin. In case of Kyogre it will be placed underneath the ocean bottom, containing prismarine as walls, four waterfalls water as a floor and giant kyogre statue in middle of cave. Right-clicking on statue with blue orb result animation of cracking stone, and blue glowing from cracks. A few moments later Kyogre is alive, and will engage you to battle. In case of groudon, cave will be placed deep under desert, contain netherrack instead of prismarine, lava instead of water and statue of groudon instead of kyogre. Reviving gro/ky will consume orb, and pokemon will be primal when battling, but lose primal status after beating/catching.
Ray would spawn in sky pillar (new structure spawning in extreme hills only) On the top of pillar there would be single ruby block, and saphire block. In order of battle Quaza you need meteorite (obtainable from catching deoxys), kyogre and groudon. When you are on top relase Groudon and Kyogre from balls. There will start battle (with animations of using Percipe Blades and Origin Pulse). Ray will come down to stop it, but it can't do anything. Feed Quaza with meteorite (that will cause it to mega evolve). Quaza will stop Groudon and Kyogre, causing it to return to balls. Then it (finally) attack you. (Quaza can't be engaged to battle without meteorite, and will retain mega form when you battle it, but lose it after catch. To mega evolve it again you must teach it dragon ascent second meteorite don't work.)
Naturally spawning mew isn't that bad, but i have cool idea for her. Mew would spawn only in jungle, but in new structure called Stone Tree. Stone tree would contain large log made from stone (log would contain even stairs and corridors) and crystals (unbreakable) instead of leaves. In log there would spawn fossil pokemon (expect aerodactyl) treated as rare boss pokemon, but all would be aggresive, won't drop anything, be um... made from red jelly... (i don't know how to call that thing. I mean this red thing from film: lucario and the mystery of mew) and for bigger hardcore there would be impossible to run away from it and using repels won't work for it. After getting away from log, you will get to the four chambers in leaves. First three will contain regis treated ans legendary bosses, being agrresive and won't dropping anything. After beating regis you will get to the last chamber, when leaves mew (but it will be on really low lvl and be timid instead of aggresive)
In order to find regi trio first you must get to the Sealed Chamber. It will be located in Deep Ocean (y<20). But when you're surfing above it there will show big message on screen: GO DOWN HERE. When you or pokemon you surfing at touch the bottom there will show another message: DIG HERE. When you do that you wil get to the chamber. It will contain braille message telling you to return here with Relicanth and Wailord. Return to chamber (messages won't show again so better save coordinates if you don't want to seek it again) Place Relicanth on first slot of party and wailord on the last slot.
That would result a short earthquake. After earthquake chambers of regis can be spawned.
1. In order to get regirock go into mesa. In mesa (y<32) regirock chamber can spawn. To get regirock get a pokemon that can learn strenght (it don't need to know it). Relase it from pokeball. Regirock will battle you.
2. To get regice travel to ice plains (y<32). Find his chamber and stay completely still for 2 minutes (real time). Regice will attack.
3. For registeel mine in extreme hills until you get to the y<32. Find his chamber and then mount a pokemon from gliding section. Registeel will challenge you.
4. Regigigas can be obtained when you caught all other regis. Give regice a nickname and something cold to hold (snowball, never-melt ice, casteliacone etc.). Go to chamber where you found regice and relase regis out of balls. Regigigas wants to battle now.
To get Zek/Resh you must get Dark/Light stone. Stones are drop of legendary and ultimate bosses. After getting it you must awake the Dragon. Go to Dragonspiral Tower (structure spawning in mega tajga) and get to the top. Dragonspiral like Stone tree have defending pokemon. This time it would be dragon type pokemon (like in Stone Tree there would be treated as Rare bosses, won't drop anything, being impossible to run away from it and repels won't work on it, however it won't be from red jelly xD)
On the top of tower awaits Kyurem, but treated ad ultimate bosses and won't dropping anything. After beating him there would appear special shrine. Plane Dark/Light Stone in it and observe beautiful animation of awaking Zekrom/Reshiram. After awake it will behave like wild pokemon and can be engaged to battle.
In mesa on height y<16 lies an strange cave with green lake. Enter the lake. One second later zygarde (snake form) will slowly raise from it, change form to the complete formand attack you. He will be treated as ultimate boss and won't drop anything. After beat there would show animation of green light escaping from it's body. After animation Zygarde core as an item will appear in your inventory. Under name of iteam there will be shown some percentage. After beating zygarde all over world have appeared zygarde cells. It's shown by green glow on the ground. You can right-click on it with zygarde core in inventory. Cell will disappear, but percentage of core will rose by 0,5%. After getting at least 10% you can right-click with zygarde core if you have empty party slot and poke ball in inventory. Zygarde will appear in ball in his dog form. If you do it with at least 50% zygarde will appear in snake form, with 100% will apper in ball in snake form too but with power construct ability instead of aura break. If you put zygarde in ball when it was in 10% form, percentage will be still shown, but on summary and collecting cells will still raise percentage.
Thank you for reading this. Sorry for any mistakes in post (ima poland heh). If you have any other ideas for legends or want to improve mine comment below :) .