It also doesn't run OS X, and lots of other stuff. If you try to understand it as "value for money", then there are far better computers for number crunching that are way cheaper than a Mac. Instead with Mac you get lots of marginal returns, that, if you have the money can appreciate, and they are all focused on things other than raw performance per dollar.
Weight, size, construction, design, no crap ware, magsafe (rip), great trackpad, first to get hi-dpi screens, first to get modern more powerful ports, first to ditch legacy stuff, and good battery life (despite some recent problems it has been traditionally better than the PC competition, even for units 2x the size). Plus a whole ecosystem that has the same values, of smartphone, tablet, watch, desktop, Cloud services, etc. And a great resale value.
Also Apple traditionally uses it bargaining/money to order the best parts of what it orders (quality assurance wise). They don't get the most powerful Nvidia, for example, but for the model of Nvidia they do get, they get the most careful produced units. Same for less/no stuck pixels on the monitors, etc. Don't have an exact reference now, but I've read that from 2 different people working for other OEMs/suppliers. Of course its also inevitable for every product run that runs in the millions that they also get some duds as they had in the past. The screens on MBPr's or iMacs have for example, have consistently been top of the crop, with respect to color, brightness, etc compared to other (cheaper or not) laptops. Compared to dedicated pro screens that cost the same as the whole MBPr just for the screen, no, but that's not the point. The point is in the balance.
Even not having to bother with 200 customization options is a feature for some.
About the "it's not thin and weights 1.5 pounds more". This might seem like OK tradeoff to you, but is enough to drive some people crazy, like this guy:
I’m have to admit being a bit baffled by how nobody else seems to have done what Apple did with the Macbook Air – even several years after the first release, the other notebook vendors continue to push those ugly and clunky* things. Yes, there are vendors that have tried to emulate it, but usually pretty badly. I don’t think I’m unusual in preferring my laptop to be thin and light. I’m personally just hoping that I’m ahead of the curve in my strict requirement for “small and silent”. It’s not just laptops, btw – Intel sometimes gives me pre-release hardware, and the people inside Intel I work with have learnt that being whisper-quiet is one of my primary requirements for desktops too. I am sometimes surprised at what leaf-blowers some people seem to put up with under their desks. I want my office to be quiet. The loudest thing in the room – by far – should be the occasional purring of the cat. And when I travel, I want to travel light. A notebook that weighs more than a kilo is simply not a good thing (yeah, I’m using the smaller 11″ macbook air, and I think weight could still be improved on, but at least it’s very close to the magical 1kg limit).* (Linus Torvalds)