It would be senseless to get rid of features, even if only 10% of users needed any particular one. The reason is one feature is for 10% of users, another feature for a different 10%, etc. There is nothing untidy about having a connector not used, and in fact almost everyone has some connector or other not used. Your ver 1 board reminds me of the PC Chips econocrap boards.
It would increase costs to get rid of features, because you reduce the desirability of the product, the sales rate per R&D and manufacturing costs, to an extent that exceeds the cost savings of leaving off a 50 cent connector. It would be different if expensive silicon were needed to support the features but it is not, you'd just waste capabilities of existing silicon on the board in many cases. It is not likely they'd get rid of layers by only removing what you suggested, a layer is still needed to support the rest, it's just a matter of which areas it covers which means no practical gain. You don't mention any particular layout issues, as it's obvious they did succeed in making the original board so acting as though it is problematic is defied by the direct evidence, that it exists.
BTW, I fully support the idea of having parallel and serial ports too. Never get rid of a feature unless it is mandatory in order to support some other more desirable feature. Since practically nobody has as many PCIe cards needed as slots in your example, but most veterans own several PCI cards they'd like to reuse, even that makes no sense today contrasted with years from now (just as it was with ISA slots slowly becoming fewer with each generation of boards).
Lastly, please keep the same topic in the same thread. This thread should just be locked as it is redundant and looks a bit like trolling. You remind me of someone who trolled on this topic previously, and perhaps have been banned since then so you created a new user profile? Sorry if that seems mean spirited but some coincidences, aren't.