Only thing I dislike about runes is extremely early game, there are some bugs with certain champs who want a different stat early (Like bard who likes early AD), and dark seal stacks not counted towards adaptive. Only thing old runes did better were quintessences, which no matter how you changed them your quints were viable.
All the other runes were crap that were basically shoe-horned into having and thus new runes are far better than those. Only thing I would changed about new runes is have one empty slot on the secondary rune page, let the first rune page give the stat bonuses (Adaptive stats/AS/HP/elixir buffs) but the second rune page this open slot you can directly put in a quint(this quint has a tad more than 1 of the old, maybe 2 old Quints=this new quint, the inspiration tree would amp this quint into 3 instead of 2 old quints) into this slot. That alone is the only thing I would do to this system to bring back the quint's customization.
Aside from early game bugs and losing quints, the rest of the game is better runes-wise. Just a few things need a tad tweaking that's all. But it's far from being an overall failure.