Here's my list from the rarest to easiest to find legendary:
1. Rayquaza! Given the fact that it's a flying Pokemon it makes it extremely rare to spawn coz air Pokemon have a maximum limit of 2 at one time in the world. Also, Rayquaza spawns at Dawn/Dusk which is just 3 mins in a Minecraft day (1.5 Dawn +1.5 Dusk). 3 mins in a MC day and with a limit of only 2 air Pokemon at a time per world i think it takes the first place without a doubt. With 1/22000 (chances to spawn) x2 (being an air Pokemon) in 3 mins per MC day Rayquaza seems impossible to spawn.
2. Lugia! Again air Pokemon, so same difficulty, but this one can spawn during the whole nightime, which is 7 mins in a MC day, so it makes it easier than Rayquaza. Also, Lugia needs a land area to spawn, coz air Pokemon can't spawn directly above an Ocean/Deep Ocean biome, so in order for it to spawn you must make some kind of platform above a Deep Ocean biome. Otherwise you will get only Kyogres.
3. Ho-Oh! Another air Pokemon but with a spawntime at daytime, so 10 mins per MC day. So a bit easier than Lugia. Btw, with the daytime Pokemon you have the advantage that you can sleep in the bed to skip the night. So you can technically have daytime all the times. But still the fact that it is an air Pokemon makes it by default harder than other nightime Pokemon, coz of the 2 per world thingy.
4. Raikou! Land Pokemon but it spawns only during Dawn and Dusk time which is 1.5 + 1.5 = 3 mins perm MC day. Ofc land Pokemon can be 40 at a time in the world, which makes it more spawns that water Pokemon per time, and the only water legendary Pokemon is Kyogre which spawns at nightime, so 7 mins per day. But I belive that 3 mins per day against 7 mins per day overpowers the 40 spawns per time against 20 spawns per time, so I place Raikou above Kyogre just for that reason.
5. Kyogre! For the reasons I mentioned above. Water Pokemon with 20 spawns per time and just 7 mins per day to spawn (nightime)
6. Suicune! Again spawning at nightime so 7 mins per MC day, but unlike Kyogre this is a land Pokemon so it has more spawn chances per time (40) unlike Kyogre with 20.
7. Mew, Groudon, Entei, Selebi! All of them share the same conditions. Daytime spawn (10 mins per MC day) and land Pokemon (40 spawns per time). Easiest of them all. Only the biome rarety matters here.
Any thoughts? I believe Pixelmon onwers should chance something in air Legendary Pokemon spawnings coz they seem way to difficult to spawn, especially Rayquaza.
What legendaries do you own? I managed to get 2 Groudon, 1 Suicune (actually found 3 but the 1st got glitched, the 2nd got lost; never found where it spawned and it despawned, and the 3rd is the one I have now), Entei and Raikou! Now I am searching for Lugia. :)