Ok found a fix!
We can't recruit Moltres and other birds because we don't have their Friend Areas. Normally they are supposed to be unlocked when recruiting them, but here their recruitment rates seem to stay way below zero, even with a Friend Bow. To fix it just use this Action Replay code to unlock all Friends Areas (EU version):
Now recruiting them is possible, but that problem with recruitment rates being extremely low is still there. Fully evolved Pokémon have the same problem. The only fix I've found is to use this 100% Recruit Code
IN CONJUNCTION with a Friend Bow. Without the Friend Bow you can recruit any Pokémon who didn't have their recruitment rates modified, but to recruit legendaries and fully evolved Pokémon (and any previously impossible to recruit Pokémon), you'll need to combine this code with the Friend Bow.
You have to activate this code BEFORE climbing the stairs, else it won't work. You will then be directly led to the room which contain the stairs, which sucks, but everything will be 100% recruitable on that floor. So I recommend activating it only before climbing the stairs where lies the Pokémon you want, if you don't want the game to become too easy.
So yeah, we go from a 0% rate to 100% but thats the best tradeoff available now since this hack seems unfortunately abandonned.