Usually, if I have trouble comprehending something at first, if I can pick bits and pieces out and say to myself, "Oh, okay, there are some actual ideas here, there's something to be understood in this," then I can admire a film's ambition and connect to the ideas that I do perceive. With Synecdoche, even though it gets clearer with time, I was befuddled on some parts immediately after. However, it was a befuddled that I thought was my fault, not the film's. Some films intentionally befuddle you in order to cover their lack of true substance, their lack of true things to "get."
This of course is all subjective. But if I don't get it, and I've looked closely, and I have determined in my opinion that it's not my fault but rather poor execution from the writer/director/whoever, then I am quick to say it's a bad movie.