To remedy this riot could disable specific runes for specific champions. This would also help to prevent trolls with bizarre rune pages that just don't benefit their champ at all. This way the runes would work for the champs they were intended for and won't become abused by champions that weren't intended for them in the first place. However this would take away a lot of diversity.
Alternatively riot could be really bold, scrap runes all together and bring augments into play - champion specific trees. It'd be a lot to keep track of, a lot of work in terms of coding and spell effects... but it'd be much easier to balance. It would also seriously cut down on trolls. Personally I think the positives outweigh the negatives. It all depends whether or not Riot feel as though they have that kind of time and resource to invest into something people may/may not like.
As far as I can tell though, the augment system during the Odyssey game mode got a lot of positive feedback. Of course trolls could still buy stupid items, but that's off topic so I won't touch that. It'd also mean there's no 'wrong way' to set up the champ specific augments because they are designed with that champion mind. It would all be down to preference and what the player felt worked the best for them. This way it doesn't take away from the diversity and gives you a level of personal customisation with the champ you want to work with.
That's just what I think anyway. But yes. It gets particularly annoying when they completely gut something good they introduced. Fair enough if its broken but sometimes I swear they just gut things that just worked well, not that were necessarily op, to the point that they are actually useless.
I've seen a lot of people asking for augments so perhaps if enough people ask we can get something that might actually stick for once :P