I am not so sure if we had suffered from the same problem. My problem was: when switching from one desktop(workspace) where iterm2 resides to another desktop ( where I may want to check some documentation or browse web), iterm2 always shows on top of the new desktop and covers the application on the new desktop. This is annoying in a sense that whenever I want to switch to another desktop, I must want to use something on that desktop(which is definitely not iterm2 as iterm2 is on my current desktop) or I just want to have access to the desktop. And when iterm2 follows, it just screws my will and I need to manually hide or close it, which can be really annoying when you do the switches thousands of times a day.
And the solution to this is actually quite simple. According to my observation, as long as the iterm2 is not on the second place of the application switching list(the list that shows up when you cmd+tab), the annoying behavior doesn't appear. So what we need to do is to exclude iterm2 from the switching list. And there is a nice option to configure this in iterm2's preference panel, under the appearance tab.
And the checkbox on the bottom most is what we want!!!
I just found out the answer now and I am so happy that I finally figured it out! I had been annoyed since 2013.
Problem with this is that it requires spaces which means you can't have a window open wide taking both monitors' space. – Pithikos – 2017-07-28T10:48:21.613
That's it! I've been annoyed by this for a year now! – duckworthd – 2014-04-13T18:52:49.100