So with all this in mind, let's talk about what i'm doing with my runes/masteries for LANERS:
== Reds ==
For ADCs, i still think that you're going to want to go flat AD reds. Most Trinity-ADs tend to have a lot of mixed damage, so they don't gain as much from Armor Pen, and the extra AD is always going to be important for last-hitting and pushing towers in midgame.
However, i think that flat ArPen reds are going to be much better for toplane - mid AD Assassins will probably want to keep their AD since they tend to struggle with last-hitting early game without starting with a bunch of flat AD to clear with spells. Excluding top-lane smite shenanigans, top laners still frequently take TP. Combined with the level 1-3 changes, there's just not a huge amount of kill potential there. However, when you hit level 6... then you'll really want that Armor Pen (or Hybrid Pen if you're a Jax/Renekton/whatever. You only need ~30% of your damage early game to be magic to break even with ArP, and only 10% of your damage end game).
For mages mid-lane, Hybrid Pen will be slightly weaker due to the AD nerf. It might still be worth it if you're planning on being aggressive with autoattacks (building a Sheen or playing Ziggs, Fizz, etc), but one of the big reasons to have at least 3 HyPen marks before was to help with last hitting. But since minions no longer have armor, that doesn't really help. If you're playing someone like Vel'koz or Karthus mid, who have short auto-attack ranges and tend to be focused purely on spells, pure MPen is probably better.
Supports have a few options. i know that towards the end of the last season, AD marks became pretty standard on supports, due to how important fast-pushing to level 2 was. However, they are going to be really affected by the "4-17" dip, since they are going to be trapped there for a very long time, so they are just going to be even more squishy (assassins go "nomnomnom"). For more aggressive supports, Hybrid Pen might be better just because that will give you better scaling (espiecially on Sona). Armor reds are always a reasonably good defensive option and might keep you alive against Trinity Force carries (they are only 10% weaker than yellows). i'll probably end up going a mix of AD and Armor since i tend to play pretty aggressively with autoattacks on sustain supports.
== Yellows ===
You basically get a "free" set of flat runes at levels 1-3. By the time you get to level 4, per-level runes are nearly as good as flat. Unless you're going against an extremely aggressive level 2 lane (Leona + Graves/Lucian), or going against someone who might have ignite, there isn't a huge incentive to take a lot of level 1 flat defensive runes. Plus, i think junglers are going to need stronger leashes, which will reduce the level 2 fast-push => all-in strat (... i hope). Mid lane might start going back to leashing, at least for passive matchups.
So, i think that flat hp seals are a LOT weaker than they used to be. With the rune rework a few months ago, Ignite was pretty popular still in top lane / support. And flat health was really good at stopping that + the omnipresent level 2 all-ins. But you don't really need it anymore, imo. The only time i'd take flat health seals is with a mix of flat Armor seals against aggressive lanes (6 Armor, 3 HP). Scaling HP is still pretty good, and it's one of the best ways to deal with the overall stronger Abilities you will be seeing in teamfights.
So yeah, i think Scaling HP will sort of be the "default" (espiecially in midlane), with the alternative being 6 Flat Armor + 3 HP for botlane and against aggressive laners. Armor/lvl is pretty good if you think the first 4 levels will be passive and you're going against an AD opponent (or if you're using DShield/Crystalline Flask). A mix of flat/scaling Armor could be an interesting alternative for botlane depending on what supports become standard.
=== Blues ===
i think that blues are mostly unchanged for everyone except midlane.
Toplane: CDR blues if it is AD v AD, MR blues against AP opponents, MR/lvl if you're the team tank or against hybrids.
ADCS: standard mix of MR + MP5. Maybe MR => MR/lvl if botlane becomes really passive and double AP comps become standard.
Support: standard personal choices of CDR, MR, Armor, MP5, AP/lvl. Support blues have been shitty forever...
Mid: If you're going Athenes, AP/lvl is probably still your best (unless against an Assassin). Flat MR will be a bit weaker due to the 1-3 changes. With the new mid-game spike of abilities, using pure scaling MR might be fine, and perhaps optimal. There's a strong possibility Morello + Tear will become the new standard build midlane (once they fix the Chalice 5x MP5 bug), and scaling MR works really good for that. If both laners rush tear, kill potential is going to be pretty low first 9 levels. MP5 yellows are an interesting option and might turn out great on certain champs (espiecially on Velkoz combined with MPen reds).
=== Quints ===
Like blues, i think that they are mostly unchanged.
Toplaners will still probably go AD. AP tops will still probably go MS (or occasionally AP for like Lulu).
Midlaners will still all go AP/AD, with the occasional MS for skill-shot based matchups. 2 Armor Quints + 9 AP blues is really good against AD.
ADCs will probably still all go AS. You might see +1 AD quint to help with the ~2 AD nerf. Lifesteal might be slightly better now though (minions have higher hp now, can lifesteal slightly more, lifesteal is always better midgame than AS except for killing towers/dragons/barons). Maybe 2x AS + 1x LS/AD.
Supports will probably keep 2x Armor with 1 HP/MS/AP.
=== Masteries ===
Masteries in general are probably unchanged for laners. Double-Edged Sword might be a little bit better for non-ADCs due to the whole 4-17 ability spike (though i still think Feast is better).
The one change i will be making for mages will be Runic Affinity => Culinary Master. Since i'll be taking more "greedy" per-level runes, combined with the blue-buff duration nerf, having a buscuit will help in case i screw up early game, as well as helping deal with poke a bit better in mid-game. It does weaken me end-game since you lose 24 seconds of blue buff...