Shrug I'd agree you can definitely find fault with many of the programs that currently exist on the command line though every single one is still miles and miles better than a GUI -- if you're going to do something one time, it's great to click a checkbox like 'show hidden files'. If you're going to do it regularly, it's worth looking up '-a'. If you want to do something unusual it takes a minute or so looking up the command's help. Whereas on the GUI if you want to do something unusual, the answer is generally "whelp, sorry, learn CLI peasant you just can't do it since I didn't anticipate your weird need and spend time rendering a menu choice and 4 interface screens with click boxes so you wouldn't have to type anything".
If GUIs had as many options as command line programs did they would be completely unusable trash, with an enormous unintelligible control panel, and you'd be looking iconography up in a reference manual instead of switches (have fun designing all those icons and having different ones express different subtle alterations in how a command will execute)
There are a lot of options because the tools are flexible and capable of expressing MUCH more than a GUI. I'll give you there are some consistency issues, but they are historical not fundamental to the CLI. I'm honestly surprised someone hasn't written a wrapper to standardize every app in a shell so they all use the same format (ie have a 'one true format' for argument passing and just convert as necessary for every CLI app, parsing their manpages as they are installed if necessary), it wouldn't be very difficult. It never occured to me (or anyone else likely) because it just isn't a problem. You try to use a program one time, it doesn't work the way you expect, you look it up, it takes 4 seconds, if you use it a couple more times then you just know.
Scripts don't run away from the command line, they embrace it . Scripts are the reason you use the command line; it's just text, so once you can do something once you can do it as many times as you want and share it with others instantly. Have you seen a macro to automate a GUI process? That moves the mouse around and clicks on stuff? And breaks constantly? Probably not, because nobody uses them.
Once you get into a command that's long enough to type into a file you've already written a program and sure if it's worth saving people will save it. The CLI blends using a machine and programming it and IMO that's a good thing -- it promotes literacy instead of encouraging people to point and grunt at shiny menu boxes and to refuse to learn how their machine actually works. If you're doing research and your main tool is a computer, it pays to learn how it works. It's not exciting but it's the same in every field. If you want to become an expert you need to understand your tools on a deep level.