I personally don't like the current rune system as it takes an insane amount of time to properly rune a hero due to the poor layout and propensity for getting runes with stats that don't make sense. As such I've only runed a few heroes and rely more on team synergy to advance rather than developing runes. Most of the time I'm at or near the rune cap (500 if you want to know) and have a hard time figuring out what I really want on a hero.
I don't like the cost of removing higher starred runes as it keeps me from experimenting with different runes on a character. I can understand a small flat fee for removing any rune but the scaling based on star should not be there. These costs actually have kept me from fusing runes because i don't want to waste runicite but a low star rune doesn't really let me test it out either.
Maybe I'm just being a baby about them. I just don't feel like I have the time to properly invest in the current system so I skip it for the most part.
One way I've thought that would be more useful would be to have a system that binds a rune to a hero and limits the runes to a set of stats that that hero could use. Maybe this only includes the secondary and tertiary bonuses. The advantage of a bound system would be that stat bonuses on runes could be balanced for the specific hero. i.e. starting energy runes on trio, spider, kaiju etc might be reduced compared to someone like corgi or dh.
I do agree that directly picking stats or allowing reroll of a single stat may be a bad thing. This would encourage cloning runes thereby reducing the variety of builds to only a couple for each.