for future reference, here is a post explaining how the current legendary summon system works.
being able to recruit legendary pokemon has been a long standing controversial topic in the history of pmu. it is no surprise that players want to be recruit legendary pokemon and train them just as much as the staff have had their own reservations on the matter.
in the original pmd series legendary pokemon hold their pedestal status because there exists only one of each of them. they are typically either guardians (boss) of dungeons or have created homes deep inside them. it makes sense to be able to recruit them in the original games where the entire story line is centered around you - the only player in the universe. however in pmu’s unique mmorpg setting teeming with hundreds of players it does not logistically make sense for an individual to permanently be able to recruit a legendary pokemon. if you recruit rayquaza and he is sitting in your assembly, who is guarding the top of sky fortress and dropping loot now? what happens when more players such as yourself enter its lair and how is he still there? why are there five other rayquaza’s sitting in town? what happens when you (a rayquaza) complete sky fortress again only to find yourself in a battle against… yourself? unlike the trainer games, the pmd series is very particular in its treatment of mythical pokemon. they are colossal titans wielding unparalleled power, have unique personalities of their own and even so much as encountering one is a novel experience on its own. in fact, similar to gym leaders in trainer games, the story line in mystery dungeon is focused around completing dungeons and defeating legendary beasts which gives the pmd series its characteristic charm and appeal.
understand just how easy it would have been for staff to make legendaries available like any other recruit. they would not have had to think of a creative process of obtaining them, spend hours coding a complicated mechanism, seek a middle ground between community and staff members in favor or against making legendary pokemon available and of course it would have been an easy cop out from actually churning out new and unique content/game mechanics. the slate system offers a workable system that doesn’t break the universe the game exists in but also allows players to enjoy being a legendary by summoning one for help.
by now i feel i have made it abundantly clear that for the sake of preserving the integrity of whatever plot/storyline pmu has left resembling remotely to the original pmd series, legendaries should not become available in the same way as regular recruits. i am however in favor of having cheaper fusion prices and players being able to customize movesets on the legendary pokemon that they have fused which would be slightly tricky and time consuming to implement but still possible. this would allow room for interesting ideas for example having crogunk swap shop in caustic sewers break point or electivire shop in thunderstorm forest so that players have to put in effort to get their choice of permanent moves on their favorite legendary pokemon. additionally more purpose and utility can be added to legendary pokemon by allowing them to be summoned in the arena for competitive battling/legendary tournaments or having parts of a dungeon that can only be accessed by specific legendary pokemon to obtain a coveted pokemon/item to add a layer of complexity to user experience.
(note: while phione is available in pmu, it is at most a demi-legendary pokemon of debatable status given how it exists in extension to manaphy and is not ‘rare’ as it exists freely in the wild.)
cheers