So it seems we're going to get the current unlockable rune effects on the skills. It's a satisfactory solution to their problem but disappointing in that rune effects are not something you will be actively progressing (a singular rune effect that gets better ) They decided to lock them in at about what would have previously been a level 4 (5?) runestone.
I find it hard to believe they will leave it this way over time (years). I would suggest the following:
Each rune for each skill is assigned a progression bar (think xp bar) - the rune effects (green numbers) will progress with each filling of this xp bar (similar to how the old runes scaled).
A generic "rune dust" type item would drop in game and be worth a certain amount of rune progression points (RPP). As an item they would be of a "rare" category - not dropping like candy - but not "OMG I've played for 4 years and never seen one drop (ala: Windforce)
The first level of a rune progression would require a modest input of dust - say the equivalent of 20 drops - say 20 RPP's. After that each additional level would get progressively more expensive - second progression would be at least double that amount.
The system above would be the most "hardcore" - your input into a particular skill+rune effect would be permanent and unchangeable - changing to a different rune effect of the same skill would require new investments of time/dust.
One step down would be a similar system except you level a skill (not a rune) and all runes effects within that skill level at the same time. This allows you to change effects easily but not skills.
Even easier yet would be leveling entire "categories" of skills as they are broken out on the Skills Tab in the beta - all skills on that same tab would level at the same time including all rune effects. - "All Primary attack" or whatever.
Total Newb Mode would be a singular SKILL/RUNE xp box with ALL skills and runes leveling at the same time (obviously the amount of dusts used would need to be correspondingly higher given how much would change). This fits in with their "No permanent mistakes" philosophy of D3, but to me it's the least interesting - and frankly I'd rather have nothing than this last option.
The idea is pretty nice, not so innovative but cool. But you forget one thing, they want us to be able to swap skills and be able to choose every other build. And with this scaling of something which affects your power, some builds become obsolete. So if such change is made, it's the same as bringing back the old skill tree point system.
Something I think might be neat to go along with, and slightly modify, this would be a different type of skill XP. Instead of increases being derived from item drops, it should in addition come from longtime use of a skill. Use the skill a lot, build XP to increase it's level. Obviously the amount gained per use would be very small, but give you something to work towards. Switch the skill out? Lose all XP for it. This would provide the best of both worlds in giving people the ability to switch skills at will but still have some penalty for doing so. Or rather a reward for not doing so.
Your first suggestion is pretty good. It's probably better than what Blizzard will actually end up doing. You would have to not make the rune choice permanent though, but other than that it's fine. You could just let the player keep using the dust on different runes.
Blizzard has to find a way to make it so the actual rune effects aren't displayed on the items themselves because it gets too complicated.
In my opinion, they're just going to add a + Rune Level affix to weapons and armor. So basically you'll only get increased rune effects in Inferno or something where the + Rune Level items drop.
And perhaps they'll change the number of rune levels from 7 to like 30, or even higher. So you'll have some players running around with +7 Rune Levels, and then you'll have more elite players with +25 Rune Levels, etc.