while that makes sense on an item, I would venture to say that all the runes should cost roughly the same within their own category, by importance, So yeah attack speed reds are correctly priced but attack speed yellows could be cheaper, Ability power blues should cost the same as attack damage reds
Realistically though, it boils down to: IP is something that is attained through grinding, and before you have that amount of IP you are at a disadvantage to every person you lane against.
Since runes have massive impact (And honestly the current system should be replaced), then we can't really justify the items being so... gated.
Just give everyone all the tier 3 runes, there is literally zero reason as to us not having them all.
OR
Incorporate the mastery system with the rune system, unlock up to seven quints starting with just one. Store the quints on the champ