It is a huge loss for AP champs, and the changes aren't on PBE yet because APs are going to need a lot more individual work. Possible reasons:
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APs almost universally run pen runes and masteries, but most ADs start AD instead of lethality.
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Pen is a variable-scaling stat, not a fixed-scaling stat like AD or AP. For example, let's look at a few mpen values vs a variety of targets:
Standard mage runes/masteries at max pen
Enemy damage reduction with 44 + 35% mpen vs. enemy MR:
10 MR: 0%
20 MR: 0%
30 MR: 0%
40 MR: 0%
60 MR: 0%
80 MR: 7%
90 MR: 13%
100 MR: 17%
150 MR: 35%
200 MR: 46%
Full pen mage runes/masteries/items at maximum pen
Enemy damage reduction with 56 + 35% mpen vs. enemy MR:
10 MR: 0%
20 MR: 0%
30 MR: 0%
40 MR: 0%
60 MR: 0%
80 MR: 0%
90 MR: 2%
100 MR: 8%
150 MR: 29%
200 MR: 43%
All mages post-patch at maximum pen
Enemy damage reduction with 30 + 35% mpen vs. enemy MR:
10 MR: 0%
20 MR: 0%
30 MR: 0%
40 MR: 0%
60 MR: 8%
80 MR: 18%
90 MR: 22%
100 MR: 26%
150 MR: 40%
200 MR: 50%
Damage loss to standard mages
10 MR: 0%
20 MR: 0%
30 MR: 0%
40 MR: 0%
60 MR: -8%
80 MR: -11%
90 MR: -11%
100 MR: -6%
150 MR: -5%
200 MR: -4%
Damage loss to full pen mages
10 MR: 0%
20 MR: 0%
30 MR: 0%
40 MR: 0%
60 MR: -8%
80 MR: -18%
90 MR: -20%
100 MR: -18%
150 MR: -11%
200 MR: -7%
The takeaway here is that the value of starting pen is extremely difficult to quantify because it varies based on the enemy target's MR, your starting pen, and flat and % pen from items. A standard mage is losing 8 pen from Marks and 1.5 + .25/lvl pen from Precision. That's 12 pen at level 10 or 14 pen at level 18.
But look at the difference 12 pen makes between the standard mage (8 pen in Marks) and the full pen mage (20 pen in Marks, Glyphs, and Quints). That 12 pen has exactly zero value against targets with 0-68 MR. Against a target with 86 MR, it's worth 11% damage. The absolute maximum value of 12 mpen is 15.6% damage.
So how the crap is Riot going to use fixed stats and ratios to make up for the loss of mpen that's worth anywhere from nothing to nearly 16% total damage? And how will champ buffs make up for the loss of mpen scaling from non-scaling or low-scaling damage sources like Liandry's, Spellthief, keystones, on-hit effects, and item actives?
In other words, it's a much harder problem to solve than for ADs, though they will almost certainly have to do a second pass on lethality-stackers.
and 
. AD usually don't get lethality in runes, while ap used to get something like 7 magic pen.
?
still waiting for a buff of any kind
will gladly swap places with Wukong. At least monkey is still playable.
kind of did. That way riot wouldn't have to go through such high calculations, I guess :D