Here is my boss suggestions, but with dungeons to balance it out
Giratina would be a new boss, with it's own dungeon, resembling Saffron City. This dungeon would also have you free Lugia (if it's playable), but also new spirits like Tyrantrum, Zebstrika, Beedrill, Cyndraquill, Sea Pipe Statue and Midbus (if this dungeon was added)
The Other boss idea would be the Ender Dragon, but only if Steve gets added, and she (yes the Ender Dragon is female) would be found in the Minecraft Dungeon, were you have to free Fawful, Dixie Kong, Midna,
, Joker and Steve (if Fawful, Dixie Kong, Midna and Steve are playable, and you have to get Piranha Plant and Joker by freeing them), plus a lot of Minecraft spirits to free.