Second question: Why did the quality of these "filler" films get better? Guardians Of The Galaxy Vol. 2 and Thor: Ragnarok could both be considered "filler" movies. Hell, the plot to the first Guardians, when you look at the broad strokes, is extremely cliche: "A group of reluctant heroes band together to fight an evil wizard / family member from blowing up a planet using a super-weapon, only to take down his spaceship and save the day." That's also the plot to Star Wars. Ragnarok is about another Asgard sibling putting together a generic skull army to take over their world ... only with an even pointier helmet. So why is it so amazing despite that oatmeal premise?
Because it's fucking weird, obviously. This "oatmeal" premise is flavored with crazy-dick characters and Led Zeppelin. Jeff Goldblum is dressed like a gospel space-priest and appears multiple times as a hologram. The movie is so comedic that it's practically a parody of itself. The studio got the dude who made What We Do In The Shadows and let him make a beautiful mess, like a cocaine toddler in a Walmart. Marvel realized they were making filler films and said, "Well shit, we might as well fill these fillers with clown guts and candy." And that's goddamn swell.
And so the rule for Phase Three came down to a successful Marvel film being either A) a unique and interesting story told in a straightforward way (Civil War, Homecoming), or B) a really straightforward story told in a unique and interesting way (Thor: Ragnarok, Guardians).