Bashiok explains lots of questions about skill runes value & gameplay in Diablo 3 , read all the answers here:
The function of runes is to slightly modify the way a skill works.
Bashiok: Some of them are fairly significant modifications, but I suppose it depends on what you think of as slightly or significantly.
There are only 5 types of runes
low level versions drop pretty frequently so its not difficult to find any particular rune modification you want.
Bashiok: Are you basing this off of videos or playable demos we’ve produced where we specifically set drop rates in order to showcase specific systems such as skill runes?
The only difference with more rare runes is that they would have an increased effect on the stats.
Why not simply allow you to select between the 5 operational modes on each skill in the skill tree? If the only effect of more rare runes is a slight increase in damage or effect, this is not a very exciting change.
Bashiok: The changes they offer approach significant change in the operative use of a skill. It also plays into an item game, they drop like weapons or armor, and together with everything help to create a random drop pool and through long-term play (and trading) you can work towards a specific character build. Just making them a switch would remove the item game portion of gaining runes, and that’s a part of the game we like playing up.
If the only advantage to a super rare rune in D3 is that it has +5 instead of +4, that’s pretty lame…and as a “casual powergamer” I don’t really care about a small difference of +1. This is going to make seeking out these rare runes a lot less fun because there is so little benefit to getting the ultimate rune…much less exciting than seeking out the runes and completing a runeword like HOTO or something, a ritual that made me FEEL like I was making real magic happen.
Bashiok: It sounds like you really liked the crafting component of runewords, and don’t necessarily dislike the skill rune system. They’re obviously very different systems and serve different purposes. As far as being excited about a +5 over a +4 stat, yeah that’s end game min-max kind of stuff, but the skill runes themselves will have plenty of excitement when you get one to drop. It’s just for different reasons. Maybe you’re a level 10 Wizard, you’ve been using magic missile as your main attack for a long time now and it works fine, sure, but… what’s that! a rune drops and it turns them into heat-seeking magic missiles, or some similar effect. That’s a pretty dramatic change, and an exciting thing to look forward to in my opinion.
Basically, in making this post I hope someone realizes just what an awesome thing runewords in D2 were and brings them back…possibly replacing D3 runes, which don’t really have any useful reason for being an item at all, and could just as easily be made as a selectable mode for each skill.
Bashiok: Runewords were a pretty cool system at their base, and yeah maybe they ended up causing some problems, but they were an interesting way to change items. But an item augmentation system really has no bearing on skill augmentations, except that they are both using the word rune. But using a word for two different systems doesn’t invalidate them.