Account level definitely should not matter in a moba. Everything a level 30 account has available and gives advantages should be available to a level 1 account. There is no reason a new player should be put at a major disadvantage versus a fully leveled account. Gating summoner spells and masteries just makes new players extremely weak for no reason.
As for runes the tier system is pointless. Tier 1 & 2 runes are literally a waste of minor amounts of gold. There is no reason to have a lower level version of all the tier 3 runes. Tier 3 runes should be available from level 1 and not cost more than 10 champions for all the necessary runes to play any champion. Literally to be able to play any champion on the roster and still be competitive at a minimum you will need to spend 50,000 to 100,000 ip. That's around 500 - 1000 matches.
My estimate to be able to play any champion efficiently rune wise would be something like this
9 of each for these
Marks: Arpen, Mpen, Hpen, Ar, Ad, As, Crit
Seals: Hp, Hp/lvl, Ar, Ar/lvl
Glyphs: Ap, Ap/lvl , As, Mr, Mr/lvl, Cdr, Cdr/lvl, Mregen
Then quints which are 3 of each
Quints: Ap, Ad, Ar, Cdr, Hp, Hp/lvl, Crit, Hpen, MS
Actually that pretty much lists every rune I've used often or on multiple pages playing every champion in at least one or two games (Only 690 wins in the normal queue tab).