Well it was noted by the forum community when the first mega1280 board was released that there were 16 I/O pins not exposed to PCB traces or pads. But being a open source project, another vendor, Seeeduino, built their version of the mega1280 board that went ahead and brought those pins to a added header connector. So for those that want to utilize such pins there is a path to proceed without having to build your own board, but you will have to supply your own software functions in some cases to support using those added pins.
To suggest that the arduino team must meet all requirements to all users in all their products is somewhat unrealistic, there are always trade-offs to be made for any engineering effort. At least the open source nature of the arduino platform allows SOMEONE to proceed if they so wish as there are no proprietary, trade secrets, or closed source code to prevent improvements.
I have several issues with most of the arduino boards such as the auto voltage selection design, auto-reset design, shield connector spacing, and that is just on the hardware side. But none of these things are show stoppers that can't be worked around or eliminated by selecting another vendor's version of a compatible design. The easy part is finding faults with others decisions, but that need not stop progress for users. It's not like you need permission to change anything you have the ability to change.
Lefty