While playing AS legendaries would break the game, fighting against them would be an awesome side-quest to a lot of dungeons. For example, Kyurem could be a good choice for an alternate Winden Forest boss (accessible via secret stairs on last floor of Winden Forest). To unlock the secret exit, you MUST have completed the dungeon first.
You’d get a list of legendaries defeated in your profile as extra perks/bragging rights.
Personally legendary’s as defeat able bosses would be a nice asset to the game but the bosses are quite strong how would you come across having them nearly equalized towards the players stats? As well I think you find this has been suggest ages ago in the past.
Nice idea tho!
I’d suggest making them about 50 percent higher in level than that recommended for that particular dungeon, thus giving earlier dungeons a chance to be replayable by higher-level Pokemon, without being essentially pointless.
Here are a couple more ideas I have come up with:
2.Customizable dungeon LENGTH. As in, you can scale the number of floors to a given dungeon up or down depending on how long a quest you want. The maximum would be 99 floors. Also, to properly complete the dungeon (and have it added to your profile), you’d have to complete it at its default floor number.
Definitely like the idea :') at least until they’re set in dungeons properly.
I can totally agree with the scaling too - 50% harder i mean.
Just to say…at the moment this wont work. As far as i know, dungeon pokemon, items, floors, even pokemon movesets (amongst many more things) are individually set/must be specified for each and every floor in a dungeon.
In 1 there’d need to be…i guess a script or coding change of some sort to do that without actually changing the specified levels for the normal dungeon? That could happen with work i think though so that isn’t the main issue here.
However with 2 there’s definitely an issue - even with a way to extend a dungeon beyond its specified things “temporarily”, dungeon floors are vastly different. I mean okay, winden forest is the example above and ill take that. The first 12 floors (i think) or so are based on frosty forest/pmd1 in design, have mostly 1st stage evolutions (a few exceptions) then after those floors theres darkness, design changes and Final stage evolutions are there. So if a dungeon were to be extended - without specifying completely new things - how would it be extended? Repeat the same things from the last “real” floor?
I think legendaries as bosses would go hand in hand with a nice storyline. That way the legends could have the prestige and atmospheric build-up they deserve. 
AFAIK, there are already some legendaries being used as bosses, but mostly for late-game or end-game dungeons, when you’d have already ascended to or near level 100.
And, an updated “PMU-dex” where Pokemon you’ve seen will be grayed out, until you defeat them (they’ll turn white).
That way, you can more easily keep track of what Pokemon you’ve seen, and those you still need to recruit (if you’re going for PMU-dex completion).
Completion of the PMU-dex is very low on my list of priorities right now, though. Maybe once I’ve trained a few Pokemon to level 100 I’ll consider going for completion.