Most Tier 2 runes have almost as much as a tier 3 rune. For example a Greater Move Speed Quint(That's tier 3) is 1.5% move speed, while a tier 2 move speed quint is 1.17%. This means 3 tier 3 move speed quints would be 4.5% movement speed while 3 tier 2 move speed quints would be 3.51. Another example would be attack damage quints. Tier 2: 1.75, Tier 3: 2.25. Totals: Tier 2: 5.25, Tier 3: 6.75. It's not a HUGE difference, and like you said tier 3 has some runes that tier 2 doesn't have, but in general tier 2 is fine. If you're going for scaling health tier 3s, there isn't really much like it since actual health tier 3s are like 72 health total while scaling health would be like 216, so comparing tier 2 health which is like 56 health isn't even close. It'd probably be better to run armor unless you were up against AP and needed the early game defenses severely, but yeah I wouldn't say that the runes are TOO far off the mark to where they're useless compared to tier 3, they can do well and I still use some tier 2 runes occasionally for runes I'm missing. The biggest differences will be in % stuff since that's based on actual stats for the most part and can scale.
I would try to get some base tier 3 runes(AD/Magic Pen/Attack Speed reds, Armor/HP/maybe HP per level seals, MR/CDR/maybe scaling CDR blues, AD/AP/CDR/Attack Speed quints). If there are champions you really want I'd prioritize them but if there's no one you want specifically I'd go for runes until you get at least those basics and then go back to champions.
