Here's my thoughts
-Suicune - Tin Tower - Level 60
- Raikou - Roams Kanto - Level 50
- Entei - Roams Johto - Level 50 - But Battle first it can't be caught yet, I'll explain.
-MewTwo - New Poke-Gym like Island - Level 80 (I'll explain the New Island Thing)
-Mew - Same Island - Level 80
The Whirl Islands should be extended, consisting of 5 Islands. An Ice Whirl Island, a Tropical Whirl Island, a Thunderous Island, An Anciet Ruin Island and Mystical Island.
- Articuno - Ice - Level 60
- Zapdos - Thunderous - Level 60
- Moltres - Tropical - Level 60
- Lugia - Mystical Island - Level 75
I'll also explain why there aren't any legendaries on Ancient Ruin Whirl Island.
Ho-Oh - Tin Tower - Level 75
***The Birds Explanation***
Team Rocket should have a Bigger Role, so once you encounter Articuno, Team Rocket comes in and steals it, The Events of Pokemon 2000 The Movie unfold, bird after bird, then Lugia awakens, and starts to battle Team Rocket, It Psychicly tells you to go to the Ancient Ruin Island, when you do, Slowking will tell you to about 3 Orbs you need to find in Johto, Once the events end and the peace is restored, Giovanni will be watching from Cinawood City, impressed with Team Rocket and He'll come with his helicopter and take them to Kanto.
After the Events, Lugia will allow you to catch it, considering you helped it with the 3 birds, but in order to catch the 3 birds, you'll have to battle them.
***The Mewtwo & Mew Explanation***
Red disturbed Mewtwo and inhabited an island south of Kanto, Mewtwo starts training, once Gold gets to the Island, Mewtwo Strikes Back events happen, but before Gold can stop Mewtwo from his rage, The Events of Mewtwo Returns Happens with Team Rocket trying to catch Mewtwo. Silver and Gold can help mewtwo by fighting Giovanni. after those Events, Giovanni rushes to the Celadon Game Corner.
***Entei Explanation***
There should be a certain amount of times you should battle Entei until it rushes to The Ruins of Alph, When that happens, go to the ruins and there will be Tv Newscasters and many trainers (including the R/S/E and Red), just watching the events of Pokemon 3 The Movie unfold, They will let you into the Ruins which are crystalized, The Unown and Entei will be inside. That's all I've thought up so far.