The reason is quite logical. In any arbitrary case of new replacing old. We clearly understand the old since we have much experience with it, but we don't have experience with new things. So when values are lauded of the new things replacing old things, it's difficult to understand these values since it is new. Yet people clearly understand what values of the old is being lost.
It is possible to overcome this boundary if the value of the old is so minimal that even the uncertainty of the value of new things overpower it, but this is not such a case. Whenever there is going to be an equivalent replacement, the notion of replacement is an issue in itself.
It's not an issue of pure logic, but rather the difference in certainty. this wouldn't be a problem if the new has much more certainty than the old. For example, this most likely wouldn't rile up someone who is new to League of Legends, thus never experienced the before and after. Also, this wouldn't be a problem if everyone had equivalent experience with both new and old things. The fear is if this will remain true for people that have massive amounts of experience rather than no experience at all.
Until some very reliable value is found by the community that this new rune system has that is impossible in the old runes/masteries system, this disappointment will never change. I'm personally already satisfied with this since this style of runes matches the lore's World Runes much better. Though, not everyone holds values like this at the same weight as me.