Well so many things changed lately, especially thinking about the rune changes now and i wonder which ones are better atm. ArP reds with early brutalizer seem to work wonders now.
I don't really see how the rune changes affected this decision at all. Armor seals were nerfed, yes, but all champions also received the difference as an addition to their base armor (-4 from 9 seals, +4 to base armor). The only difference would be if your opponent runs scaling armor instead of flat, but even then that just means armor pen marks don't scale as well in that situation and have to compete pre-6 where flat AD has an advantage.
To (not) answer your question, it really depends on the champion. Some champions have ability effects that scale with AD, strong bonus AD scalings or abilities like Tempest which scale with AD but not armor pen. Other champions have high base damage or other forms of armor shred ( Dragon Strike, Crushing Blow) which have better synergy with armor penetration runes.
Either way the difference between the two setups is so small that the better setup can vary between champions or even flip depending on the opponent's runes, masteries and items. It doesn't make a huge difference either way. Keep in mind that AD marks are better for pushing and last-hitting, and they usually give you the edge in trades before level 4.
When people say it helps last hitting they don't only mean "it's easier to make up for a lack of mechanics." It means that you can last hit the minions under tower that need higher ad values for most efficient last-hitting and that you can shove lane much easier.
I'm usually last hitting with AA on AP mid champs and don't run AD runes/masteries on them, so that doesnt really matter, however i see less people with 9 armor seals lately. Item builds aren't as sustain focused as they used to be either.
12 ArP for 8 AD seems a good trade, tho i still have my AD mark page around in case of a wild Lee Sin appears
The reason Armor Pen isn't a must have rune, is because champions don't have a ton of bonus AD to make great use of the armor pen. Fiora still gets free AD from Riposte, so armor pen works better on her.
The one thing that counters armor pen, is flat armor. Since flat armor is more out of favor now, it's possible that armor pen runes could see an upsurge
I've been mixing them lately and they work well against the harder opponents and the tankier opponents. I am not too sure though if it is the most optimal way, I just like to use those runes :p
To (not) answer your question, it really depends on the champion. Some champions have ability effects that scale with AD, strong bonus AD scalings or abilities like Tempest which scale with AD but not armor pen. Other champions have high base damage or other forms of armor shred ( Dragon Strike, Crushing Blow) which have better synergy with armor penetration runes.
Either way the difference between the two setups is so small that the better setup can vary between champions or even flip depending on the opponent's runes, masteries and items. It doesn't make a huge difference either way. Keep in mind that AD marks are better for pushing and last-hitting, and they usually give you the edge in trades before level 4.
12 ArP for 8 AD seems a good trade, tho i still have my AD mark page around in case of a wild Lee Sin appears
The one thing that counters armor pen, is flat armor. Since flat armor is more out of favor now, it's possible that armor pen runes could see an upsurge