Honestly, I think most of the hate is a pushback against the over-the-top fanaticism. For me, the biggest issue is the lack of portability (which seems to be much worse than most other places. As for the operation, yeah, I think that's right, although I refuse to sit in the drive-thru line. I park and go inside and almost always am out quicker than if I'd used the drive-thru. They also hire above the bottom of the apparel.
This article echoes a lot of what you wrote (and is funny to boot): https://www.cracked.com/blog/5-beloved-restaurants-that-are-seriously-overrated
As far as the hate being a pushback against the fanaticism, yeah, that's probably right. And understandable.
As for the article, I agree with the general take that their burgers are good but overrated. I just think he comes in way too hard on the pushback. But, again, it seems to be more of a pushback against the fanaticism than the food itself, which I get (well, that, and the need to be edgy because he has a column that people read, and I guess that's his schtick). And people who say, "oh, well if you didn't love it, it's because you ordered it wrong; you have to get it animal style" are just weird. I disagree about the fries, but that's fine. I didn't like their fries at first, but came to love them. But the thing about their fries is that they HAVE TO be eaten while hot. Once they cool down, they go from near top of the list for fast-food fries for me to bottom of the list.
But back to the article, I found this amusing:
There are burger places in this world that are so confident in their wares that they expressly prohibit customers from making any special requests. Extra onions? Nope. Hold the garlic pesto mayo? Hold your tongue, you heathen.
There's a local place here called Dad's (there are some other locations that, at some point in time broke away and are actually completely different ownership, but use a variation of the logo and have almost identical menu items, but are total imposters and not nearly as good) that showed up years ago on Diner's, Drive-Ins, and Dives, and highlighted their classic Dad's burger. IMO, best burger I've had in this area, hands down, and second place doesn't even come close. And why I mention it in connection with the article is that I remember the second time I went there, I sheepishly asked the waitress: "Um...please don't get upset if this is against the rules, but...would it be considered blasphemy if I asked for a slice of cheddar on that?"
She was happy to oblige, and it was out of this world. But it was one of those burgers where I seriously wondered whether they would entertain adding to it.