There's fairly big difference in filmmaking philosophy as well. Bay is famously known for saying "I make movies for teenage boys. Oh dear, what a crime." He doesn't try to elevate film, he's purely concerned with the superficial without pretense. I'm one of the biggest critics of Snyder you'll ever come across but it's impossible to deny that he tries really, really hard to achieve an artistic vision. I believe that vision is almost always misguided but at least he aims high. Snyder genuinely believes he's making more than entertainment. People give Bay more slack because he doesn't act like he wants to do more than get butts into seats. The former method invites way more scrutiny.
What you're describing was also inevitable to a certain degree not just because he's working with a beloved property but also the increased exposure that comes with projects of this size. MoS and BvS are Snyder's highest profile and most expensive projects by a wide margin. Bigger budgets invite bigger marketing campaigns, which is partly why a flop like Jupiter Ascending tarnished the Wachowski's so much in public perception despite being preceded by a series of flops.
