Runes that need to be removed
TL;DR Some runes cause problems for other champions to be picked/played and removing them clears up a lot of problems, even champion balance issues.
Certain runes have caused a problem that has been happening for a very long time now. The most notable cases are LeBlanc's having this level 2 burst or Nidalee's spear doing a lot more damage then expected. Now LeBlanc had her silence removed and Nidalee got a rework. This of course does not stop the specific runes from causing problems and allowing certain champions to be used for the wrong reasons. The runes are: Flat AP/AD Seals and Glyphs along with the scaling AP/AD Seals and Glyphs. In total there's 8 of them that cause problems.
The issue that they pose is that they allow champions who can attack from a safe distance, champions that need to wait a while before they can engage and champions who can cause more burst damage then you can, to deal more damage to you then they will receive in return.
Normally you would expect Armor Seals and Magic Resist Glyphs to counter this damage but it is not able to. The numbers for defense and offense for seals and glyphs are as follows: 9 flat armor for seals -------------------------------- 12 flat magic resist for glyphs 6.39 flat AD seals and glyphs -------------------16.02 Flat AP seals and glyphs 16.38 Scaling AD seals and glyphs --------- 43.74 Scaling AP seals and glyphs The numbers may seem small but to Riot, adjusting a champions base stats by 1 or 2 points is a nerf they needed. Even 5 damage from an ability at rank 5 is significant.
It also should be noted at how many points of MR/Armor it takes to reduce the damage by a percent. 50 - 33% 100 - 50% 200 - 67% 250 - 71%
For someone like LeBlanc, damage reduction is not a very strong counter early on when you have 12 Flat MR. With her Q, W and E she is able to take the 16.02 Flat AP and multiply it by 240% AP scaling when each ability deals full damage. Toss in her 15 AP Quintessences as well, along with 7.8 Magic Penetration marks and you have a lot more damage then you could negate with just 12 MR. As a more basic example Lissandra can get 165% scaling from her Q W and E. Follow the system above and it's still quite a lot of damage that you cannot reduce very well.
AD champions will also use flat and scaling ad seals/glyphs to get the auto attack/ability advantage over an enemy. If a Zed can use Q's to poke until his enemy is weak enough and finish them with his ultimate, then less (if any) defense from runes helped Zed secure a kill. Caitlyn, Ashe, Tristana, Kogmaw and Jinx all have some form of longer auto attack range. Knowing this, they are able to adjust runes to be more offensive and harass an enemy adc out of lane with little to no problems.
By removing the runes what will change? Mid Mages should be dealing more damage in several shots instead of one single burst (LeBlanc lv 2 and Nidalee spear before rework). If they do not want defensive runes then cooldown reduction along with mana regeneration runes should be chosen. More ability spam, less recalling to get more mana and you will no longer need to buy a low powered AP item just for that last 10% cooldown reduction.
AD carries would be less of a range game and more of a kit game. If Caitlyn is not over powering a Vayne early on with both power and range, then Vayne's will have more chance to go in and out for CS and maybe even Q/Tumble at a Caitlyn to give her an empowered auto attack to make her back off.
Top lane would be about health, health regeneration, armor penetration and cooldown reduction runes. Ranged AP tops would either follow the same system's mid mages do or in the cases of Vladimir, Mordekaiser and Mundo, they can go for health and/or health regeneration to stay in lane longer. AD tops like riven might go for cooldown reduction and armor penetration. Top is already the area for tanky champions so armor penetration is already balanced against them.
How does this change Riots balance system? At the moment nerfing or buffing a champion is not exactly easy. Nerfing LeBlanc's damage would stop her from being able to assassinate her target so the silence was removed. Nidalee has the same issue so her cougar form was buffed while her spears were nerfed. A champion who can go on sprees all the time might be on sprees due to the runes they use compared to others who favor defensive runes and are not able to do the same. If a champions damage is reduced then they may become ineffective for anyone without the specific rune setup. This is an alternative to the effect of, 'It needs a DFG or it is unable to be viable at all' which is not something Riot would want.
If a champion becomes out of control with too much cooldown reduction then it is easier to increase the cooldown of the abilities at early levels. While it seems like it's the abuse all over again, cooldown reduction is tied to abilities. Unlike auto attacks, abilities will most likely be up several seconds longer then their own cooldown. Late game when Riven wants to use her shield and Q to run away, the cooldown will be the same at max rank. Mana regeneration is the same. There will be a point where you have enough mana or a mana regeneration item to handle normal team fights and the runes will just assist in letting you stay away from the base longer to farm up for your Void Staff.
I know it is a lot of text but I wanted to give lots of detail into this issue. If you are unable to understand how it would work just think about using alternative runes yourself and it should come to you.
Also, in your next game if there's an enemy that is quite fed, check their armor and magic resist. If they have less then 9 armor and 12 magic resist (after removing the stats from the items they have), then you have your answer as to why they are fed. Won't always be the case but it's a factor to be noted.