My initial desire was "all the characters I play in SSB4", which I've stuck to for the most part. Only 4 of the SSB ones I own are ones I don't play, but they are characters I grew up with (or in Lucario's case, a gift).
Characters I play but don't have are Peach, Wii Fit Trainer, Lucina, Toon Link, Zero Suit Samus, Bowser, Bowser Jr., and runner-up with Ike, Villager & DK.
My girlfriend has the first 4 of those, so I can live with going for the others whenever.
As for leveling, only a few of mine are Lv.50. Specifically, my Wave 1-2 figures. My Chibi-Robo is maxed out at 6 though.
I scan amiibo with every game that uses them. Only reason I haven't used them a lot with SSB is because I always have other stuff in the way and was doing single player modes.
Unlocked all demos in Amiibo Tap.
Found all Pixel Toad's in Captain Toad.
Used figures with Hyrule Warriors to get Spinner and enough rewards to earn the "amiibo Warriors " medal.
Only used each Kirby figure once in Rainbow Curse, but mainly because it felt like cheating.
Have 13 out of 19 outfits in Mario Kart 8 (will have 16 when I scan my gf's).
Did all the challenges in Splatoon, unlocking all the bonus stuff.
I plan to use them to unlock their costumes when I get YWW & SMM.
Scanned them all into Chibi-Robo and got all their figures, maxed out the Chibi-Robo amiibo, got all figures & stages that require his amiibo.
Made houses for all my cards in Happy Home, gave jobs to some, copied items, invited them, plan to save houses and use them all in Amiibo Festival.