As far as I recall, every April Fool's prank that SE has made in recent years prior to this year has been non-intrusive, only showing up as a minor sidebar while not affecting the site's design much.
However, this year, the Time Travel Mode prank made drastic, intrusive changes to a site's design, which is not like previous April Fool's pranks. Additionally, it's enabled by default, which quite a few users have raised complaints with.
Last year's Quack Overflow and the "chat with an expert" from years back, by comparison, were simple buttons in the bottom right, with a pop-up prompt for users to activate it. The windows for each wouldn't activate immediately.
Why was the decision made to make this joke immediately activate, rather than keep it behind a prompt (much like the current "Back to the future" prompt) to activate it? In my opinion, it wouldn't have raised so many complaints, and it still would have been just as fun for users.