Ok, for this I can't say much, because every since 2010 or so I've used Chrome in place of Safari. As for iTerm2, I've tried to switch to it several times over the years (later mostly because of Tmux integration) but always found it to be buggy and reverted to the Terminal.

>Application switching focus failures: ⌘-tab will raise another window, but window focus will not follow. This has caused me to lose work. ⌘-tab, ⌘-w will sometimes close an iTerm2 tab that's behind the Safari window I'm looking at.

Hmm, haven't seen this -- and I use ⌘-tab and the ~ variant heavily.

I have seen lagginess in focus when switching full-screen apps use, and I sometimes start typing before that happens. This got a little better in 10.11 though (either faster focus switch or less transition time).

>- discoveryd: My Apple TV's network name is currently "Apple TV (5)". Macs sometimes do this too.

DNS issues I've had (and mentioned in another comment). They tried a transition to a new DNS backend which was buggy. They reverted back to the old one with 10.11 (or sometime in 10.10.x) though and has been OK since then.

>Slow laptop wakeup: I almost always have to tap a keyboard key to wake the display after opening my laptops (MBr and MBPr). Almost always. But not always.

Do see this from time to time (though it almost always works in my case).

Could be a sensor issue though -- not a software thing (the display up sensor not registering, but tap working ok).