A lot of these questions sound like they have been answered before, but for the record:
Because Qualcomm has so far refused to help out with supporting these versions of Android as they’ve seized developing the newer kernels required to pass Google’s certification for the SoC found inside the Fairphone 2. This is a battle that Fairphone is fighting as hard as they can, and the result is soon-to-be Android 7. For a three-year-old phone that’s unprecedented in the industry, so I’d recommend to also look at it on the bright side. 
Calling Android 7 totally outdated is a bit rich tbh. as Google is still very actively supporting it (and Android 6, and 5.1…). I’d be all in favour of newer, but today it won’t buy me anything yet. I suspect Android 7 will push the lifespan of the Fairphone 2 towards 5 years of a supported OS, which is pretty impressive.
Because a 256GiB eMMC sets you back €135 on Mouser, whereas 32GiB storage costs about €35. Even if bulk prices are more reasonable, the price of the phone would go up by €50-€75 for an amount of storage that not nearly everyone needs. And for those who do, there’s a μSD card reader to extend the storage Looks like you can buy a 256GiB μSD card for approximately €90, so essentially you have the choice this way. I’m ignoring the fact that Fairphone buys packages with RAM and eMMC in one die, and these might not exist in such configurations, certainly not if the constraint is that the RAM side of the chips has to remain equal in size, technology, speed and timing properties.
If you’re interested in the cost breakdown of the Fairphone 2, I’d recommend you to take a look here. It’s a little outdated, so potentially the cost of various components has been renegotiated, but the benefits of this could well be offset against hard-to-replace components that have been deprecated by the vendor and are only produced in smaller quantities against higher prices.
This is presumably dictated by the Qualcomm SoC chosen at the time of design. Back then this was the most modern option… and you don’t simply swap out an SoC in a phone for a newer one without significant redesign, testing and software engineering effort.
I think your shopping list would be very reasonable for a future Fairphone 3, because if you were to design a phone today to last for 5 years you want to address what you mentioned. The Fairphone 2 is a phone designed two years ago to last for 5 years (so three more!), and what you can (still) buy today is the result of that effort… plus an upgrade to the camera.