First off I want to say that presentation of Runes is, without doubt, complete ****. I mean, why would you even put such a god awful system into the beta? Yes, I'm aware that it is by no means the finished product but it's not even a good start. If it's completely revamped (which it should be) then why would you daunt us with the repetitive, mindlessly grind of combining random runes to get more random runes with no patterns whatsoever.
Let's look at why a system like this should be in League of Legends:
Seeing as how they were just put in...what 2 weeks ago, I believe we're supposed to be testing the functionality of the runes, not so much the rune system itself. That being said, I agree with most of the suggested improvements here. Specificallly removing the randomness of the runes and the lack of real "special effects" stemming from the runes. I happen to disagree with the idea that you can get 50% attack speed by end game from runes and even if you could, the matchmaking isn't going to allow someone with a high enough ranking to have unlocked those runes to be matched vs someone who doesnt have access to runes of the same caliber. Also if the rune system is that much of an advantage, the possibility of somone who just decides not to mess with the runes at all, matched up vs a person who uses them to the fullest, is very slim, at least to a high enough frequency to make most games unbalanced.
I also think, however, that the Riot team is way ahead of you and has most of this plotted out and 3/4 ready for implementation.
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