Personally I think balancing around runes is more healthy then removing them and completely balancing champions around their kits. Odd I know. Aside from having to fine tune every champion from scratch again, I can't really explain in words why I'd rather have runes, so I'll be going around with my reasoning by examples, or just one...
Before I begin, I have to say, as unfun many people find current League to be, I find that a large portion of league's champ pool are a viable choice to play, it's hardly ever, " here's 10-20 champs that are meta, play them or lose the game ", kinda situation anymore. It might've cost some fun for this feeling, but with that in mind...
Let's take the assassin class, usually excel in short trades, and bursting down enemies if they manage to get on top of their target. If we had to keep this kind of fantasy true, while keeping a large champion pool in balance, what would we have to do? Well most assassins win early short trades due to being able to proc electrocute, so we'd probably end up needing to buff their early game damage, but doing that in turn would also increase their wave clearing powers, or making their poke ability strong making them a, why play mages when you can play assassins kinda situation.
If we don't buff their early game damage, we could buff their resistances, but that could re-introduce the tank assassin trope that riot has already killed.
"But if there are no more runes, everyone lost some damage, so wouldn't assassins still win short trades?", could be the case yes, but this is just talking about early game, what about late game? what about if the assassin is behind?
After thinking about this example, as bad as it is, I now have words for why I prefer having runes around. They are both a snowball and comeback mechanic. They augment a champion to have an opportunistic upper ground, by having their rune ready, they can make stuff that's usually unfavourable be favourable. Some might not like it, because it might take away the weakness of a champion. Fair point, but it's opportunistic for a reason, it's not 24/7 increase damage or utility that one might've had if runes don't exists, which could otherwise make a champion too strong with said increase, or too weak without.
It could act as the reason to being able to come back on top despite being behind, because your opponent's small misplay. While the enemy misplaying could get you on top, if the gap is large enough, that small misplay would mean nothing in a world without runes, making comebacks harder then it already is. But here, even that small misplay with a large gap in levels/gold could give you the upper hand depending on the rune/champion/match up etc.
This small opportune moment, is IMO, the reason why so many champions can be viable, or at least, the gap between the strongest in the meta, and the weakest in the meta has shrunk, which is something I'd rather have if it doesn't cost too much fun, and I don't think it costed too much.
Though hell would I know, there are so many balance leverages in League that even a small change could have huge ripples in the game.
EDIT: TL;DR: Just read the last paragraph, otherwise. Runes are both a snowball and a comeback mechanic. They give opportunistic power to champions which can allow various champions to have increased damage/utility that might invalidate their weakness, but it's better than always having that increased damage/utility that could otherwise make a champion too strong or too weak. For what I see, balancing around runes allowed the gap between the strongest meta champions and the weakest meta champions to shrink, which I say is an overall good, even if it costed some of the fun factors in game.
to 
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was epic.
second wind and ult makes him a mundo with a 600 damage q
