I think the main issue, and this goes back years but is getting worse, is each field acting like it's a separate festival and booking a mix of acts, including big pop ones. West Holts is no longer a jazz/world stage, John Peel isn't just new bands, Avalon isn't just folk, Arcadia is a stage with big names instead of a visual experience, Shangri La has highly advertised scheduled lineups, the Pyramid Stage emphasises a mix of genres instead of booking just the biggest acts.
When the West Holts and Avalon fields are closed, or the entrance to The Park is blocked by people trying to get into Arcadia, or the central sections are heaving because everyone's swarming to William's Green, it has knock on effects on the flow of people around the site.
I'd much prefer if the simple rule was the most popular acts are on the biggest stages. Just put Mcfly on the Pyramid Stage at midday. It might seem more boring and obvious but it would solve so many crowd issues.