What is Happening to MPen Runes?
After many previews, dev posts, and even a blog specifically addressing the loss of niche rune pages, Riot has still said nothing about the loss of mpen (and lethality) pages for the few champs who stack pen in runes and items. Riot has specifically mentioned compensation for loss of AP, CDR, move speed, attack speed, health, and resists. For example, yesterday Meddler said:
We'll be giving all champs some extra base stats as part of the process of moving from old runes/masteries to new runes. [...] Other champs (e.g. mages) might get no attack speed at all and instead things like extra health/level or slightly increased spell damages to make up for lost AP.
So...what about mpen?
This is fine for mages that scale heavily off AP (eg Syndra, Ori, LB) or with kits that devalue mpen (eg Vel) because they will still scale hard with AP. Increasing base damage for pen-reliant champs (Zyra, Brand, Teemo) actually makes them more reliant on magic pen without addressing their horrendous AP scaling.
Beyond that, mpen and AP are not mathematically comparable stats. Let's compare the difference between a rune page with 30 AP and 20 mpen if we are lvl 9
versus
with
(1219 HP, 67 MR)
**20 mpen page with
**
Q: 95 (+24)
W: assuming two thornspitters attacking twice each, [207 (+18)] x1.5]
E: 200 (+20)
R: 185 (+28)
Gross Damage: 890 Zed's EHP: 1423 Net Damage to Zed: 762
**30 AP page with 
**
Q: 95 (+57)
W: assuming two thornspitters attacking twice each, [207 (+43)] x1.5]
E: 200 (+48)
R: 185 (+66)
Gross Damage: 1026 Zed's EHP: 1853 Net Damage to Zed: 675
The AP build only deals 88% of the pen build's damage. Now, let's see the numbers if you just delete the rune pen altogether:
**Zero mpen from runes with
**
Q: 95 (+24)
W: assuming two thornspitters attacking twice each, [207 (+18)] x1.5]
E: 200 (+20)
R: 185 (+28)
Gross Damage: 890 Zed's EHP: 1670 Net Damage to Zed: 650
In this scenario, 20 mpen from runes is worth 112 net damage. You would have to increase Zyra's base damage by ~17% to make up for that loss. Call me crazy, but that sounds well outside the scope of "slightly increased spell damage."
And this is really just the tip of the iceberg because the value of that 20 flat pen spikes after each subsequent purchase of flat pen, % pen, AP, and damage sources (eg Luden's, hextech items, FQC, Thunderlord's, etc). More traditional AP-scaling mages will suffer far less. The vast majority are only losing ~8 mpen from runes, and most have higher base damage and scaling than pen mages in the first place.
TL;DR: Many words explaining how mpen pages are significant, and Riot needs to address it and let us know it's on their radar for the rune update.