Well.. it might be a toolkit, but the one thing that stood about was that the pop-ups and tooltips it generated (at least the version I used back when I did my Nexus7) It would say "Now booting into Fastboot to unlock the bootloader...." It would not just launch of bunch of windows and commands.... it cataloged what it was doing every step of the way. I thought that was pretty cool.... I had gone through all that stuff when I got my 5s so I was using it to save myself some time... but the fact that the developer took the time to try to explain each and every step was very cool.
So yes, it's a toolkit, but it kind of does it in a way that goes "OK, I am going to do this, but here is what I am doing so you understand why and how."
I disagree with some of what you said. Yes, it is cool, and yes, it does tell you the name of the step that it is executing, and yes, it can save time for somebody unfamiliar with the process. The problem happens (and it does happen - go over to xda and a search will reveal a number of folks who are completely clueless about what exactly happened - they want to "Flash a ROM" and are running into issues. Other folks try to help, but need to know if they are sure they are rooted, and what custom recovery they have and whether they have supersu binary installed, and the user has no idea. (not saying that is the case with everyone, but I've seen enough instances of this to not recommend toolkits).
Other cases where a user used the toolkit to root, and then made some system updates that now prevent the user from installing OTA directly. Starts a new thread asking for help because user doesn't want to lose their data, and folks recommend flashing the stock boot.img or system.img. Again, the user has no idea how to flash just that image.
With a device like a Nexus 5, the steps are just so straightforward, and the process so well documented that doing the steps manually isn't that complicated. I've used that toolkit for my Galaxy Nexus
(because I couldn't get the drivers installed, no matter what... so yes, I get it. It has its benefits. But the user really should know what each step is, and WHY that step is needed.
But as I said in my earlier post, everyone has their preferences
Some like toolkits, some don't. It something goes wrong, user is often left clueless about how to fix it. On a device like a Nexus 5, the steps are straightforward enough to perform without a toolkit. But as I said, some like it, some don't.