What are your pet peeves?
First, Use of legacy build systems (hodgepodge of different development environments and in-house tools). We don't need a custom migration tool, we don't need to badly reinvent make in batch files, and so on. I've been slowly grinding through and bringing sanity, but it's very annoying work and the "well it works fine once you're used to it" is a strong thing to overcome.
Second, developing on Windows instead of a 'nix-derived OS. For daily programming, I like having terminals with reasonable tools installed and ready to go, and Powershell just doesn't scratch that itch and neither does cygwin or git-bash. Honestly, this is what exacerbates gripe one: if we were on a proper OS, we wouldn't have to reinvent so much stuff anyways.
My biggest pet peeve is that there are a lot of development technologies that have no GUI, or only a terrible half-complete GUI.
Currently I'm doing back-end development where I can get mostly everything done in Visual Studio, but whenever I have to interact with Git (which has several GUIs, all of which are either incomplete or intolerably slow) or the front-end guys (Bower/NPM/Grunt) I end up struggling in a console for waaay too long to get basic stuff done.
There seems to be this belief in the industry that it's ok if the interface is kind of rough and crappy as long as only developers are using it. Gripe if you want about Microsoft, but at least the vast majority of their tools have at least a decent GUI.
I prefer CLI tools during development because the tools tend to be simpler ("rougher") and easier to compose into pipelines. If you aren't using your tools this way, you're missing out on a lot of what makes them useful. They also are a lot easier to script and write documentation for...type this, type this, type this--okay, according to your shell history, you didn't type what we told you to and there's your problem.
GUI tools are useful for when I'm debugging graphical issues in the frontend (what is the DOM looking like starting under the cursor right now?), or need to very rapidly switch context in the backend (what are these variables set to? What is the prototype and doc for this function invocation?). They are annoying to script, and annoying to document for other developers. They also tend to be much larger and less composable than other tools.
As far as the git stuff, well, it's best used from the command-line.
While you cannot do massive things and get away with it, you can get in a long of small fixes and improvements (which can add up) and just apologize if anyone notices.
If you had to ask permission for every tiny change it may take weeks and the ultimate decision would contain the kitchen sink anyway. Instead just do what has to be done and try not to get caught.
I wish someone would invent some type of eye tracking that would intelligently assign the context to open windows on your screen(s).