Okay.

So it took him longer than he would have liked to get everyone on the Grid who wasn't already in his camp for one reason or another on board.

Also, Rinzler wasn't compiled--or presented to the general population as an Arena contestant--overnight.

That, and I've got headcanon that says he intended to take the ENTIRE SYSTEM through the portal in one go, in one eight hour window, because fff, since when does he overdo anything.

Not everyone was just going through the EZ Bake first; that's dumb. He'd need some dudes capable of actual reasoning skills to, like, lead the other units--just for a start. (Watch them in the EoL. They're not complete idiots until the plot calls for it.)

He's incapable of trusting anyone, so he's pretty much got to arrange all of that himself, and in such a way that none of the Programs on any one work detail really know what the other sections are doing until it's mostly done.

Also, he may have gotten the drop on the guy in the movie, but that Bartik? Real asshole. Thorn in Clu's side for cycles.

tl;dr It's not like Beck was the only Basic with bones to pick about being under new management.