Here is why and the key is the user input you reference is actually a small percentage of the market - ie not the average user:
1) The average user doesn't care about the interface long as it works. Skinning the UI is a way for the OEM to differentiate their product and possibly score points for a sale when being compared in the store
2) SD Cards are a complication for the average user. It is easier to push cloud services instead of confusing the user with file management.
3) Non-removable batteries offer greater capacity for the same amount of physical space. This translates to longer battery life which is more desireable to the average user over managing either multiple batteries or keeping it charge. It also allows for more flexible physical designs which helps make their product stand out.
4) The average user has no clue what a bootloader is or what unlocking it allows them to do. For manfacturers though it prevents them from loading unstable software and the support calls that result from it.
What it comes down to is OEM's are making phones for the average user and not you because that is where the money is. Be glad though you have a marketplace of choice that sees value in providing the features you value while at the same time catering to the different set of features your friend values.