You can't just insert a hard drive. You have to download the system software, transfer it to the drive, and after physical installation allow the system to initialize the drive and install the system software. Afterwords you have to perform the initialization sequence, including re-linking your accounts, redownloading games, and transferring saves.
To your counterpoint, you can also initialize a 3DS system transfer and just let it go. For the majority of system transfers, it is pretty simple. Compared to the PS4 transfer, it transfers everything for you and doesn't require re-intializing settings.
The problem comes from protected saves, as mentioned.
I'm actually on neither side here, I love my N3DS and think the system transfer process is pretty simple, all things considered. I've also done an HDD swap on my PS4 to a 1TB HDD. Both are simples, yet different, processes. The only additional steps you made seem like a mountain of work is downloading a file into a USB drive and sticking it into the PS4 the first time you turn it on after installing the new HDD. This is not a complicated step.
That's not to say Nintendo's account system isn't archaic. I had to purchase a "temporary" N3DS so I could do a system transfer and save my stuff, because I sold my old N3DS XL before my new one had shipped, and needed to ship it out for the buyer ASAP (hate to keep people waiting). If this was any other modern, non-Nintendo console, all I would have had to do is unlink my account from the console, factory reset my system, shipped, and wait for the new one to arrive.
I thought you meant that physically switching the HDD on the PS4 took > 20 minutes. It does not. Also, how is swapping HDDs comparable to account transfers? If you want to activate your PSN account on a new PS4, you just deactivate your old one and activate it on the new console. You can then download all your cloud saves, games, etc.
I love me some Nintendo; own an SNES, 64, GameCube, Wii, WiiU, GBA, DSL, and N3DS. But their account system is absolutely unacceptable, and anyone should be able to see that.
To summarize my points: Swapping a PS4 HDD is not hard. Moving your PSN account to a new console is trivial. Doing a 3DS system transfer is not rocket science, but is an antiquated system that shows incompetence or lack of effort on Nintendo's part in developing a proper online account system. It's not adequate moving forward, and hasn't been adequate for the last two generations.