Primer is not complicated, it's obfuscated. (and good)
It's virtually impossible to understand Primer the first time around.
That doesn't mean that people who complain about this are stupid and only like Michael Bay movies.
The basic plot is easy enough to grasp for a sci-fi fan. It's not even that complicated, really. But much of the detail is never shown, but only talked about in short, interspersed pieces of mono- or dialog, oftentimes in suboptimal audio quality. And the jump cuts don't help either.
There's a valid complaint about a director intentionally obfuscating his movie. If you're bent on it, you could edit "Sleepless in Seattle" in a manner that nobody gets it. Wouldn't elevate that movie.
I think - and you may disagree with me on that - it is the job of a storyteller to make sure any reasonably intelligent and focused audience will understand his story. There may be greater implications to a story, the stuff you talk to your buddies about at 2 am in a fast food restaurant after seeing the movie.
But the movie itself should be self-explanoratory. I studied film (though I ended up in a different profession) and more than one lecturer told us something along the lines of "If you have to explain your movie to a smart person, you've failed."
That doesn't make Primer a bad movie. Not at all. But would I think any less of it if I actually understood who that Granger guy was, why he followed them before they followed him, and how the hell he time-travelled......? No.
I had to write this, because reading through this forum, I discovered a few incidents where people who complaint about (parts of) the movie were dissed as dumb sheep seeking popcorn flicks, while the dissers pretended they were some movie elite.