Which is capable of more damage vs champions: +2 Magic Pen, or +5 AP?

It depends on your ap scaling and their mr. If your rotation has 2.0 ap scaling, 5 ap adds 10 damage. 2 mpen reduces their effective hp by 2% unless your mpen was already equal to their mr. So if 2% of their effective hp is at least 10, then mpen is better as long as their mr is still higher than your mpen in this case.

it depends on the champion and whether or not the enemy has mr runes or doesn't have any

This is assuming that +1 point of Penetration reduces -1 point of Resistance, correct?

Depends on the champion I would say if you have AP Ratios of 0.7 upwards then the AP is better

i'm no expert, but I guess that is the way you think about it

I would just go for the +15 AP. It will help you last-hit minions and waveclear more than Magic Penetration would with very little difference in the damage to champions.

I think 15 AP is better for quints than 6 magic pen.

500 dmg against 40 MR (base MR of most champs + 10 from runes or whatever) is 357 500 dmg against 34 MR is 373 You need ~525 dmg against 40 MR to do more (375) than with the 6 magic pen. So thats ~160% scaling and I think most AP champs have that on all their spells combined.

(btw against 100 MR your damage gets halved, so 500 is 250. With 6 magic pen you would do 257, but with 516 total damage you would already do more than that, which is ~100% AP scaling on all spells)

Well like already stated before magic pen scales into lategame damage wise but flat ap does not. So flat ap for early mpen for mid/late. Then there is the matter of ap ratio's if high then i flat ap gets stronger in the early game so if you have high ratios this is very good for early game.

The other thing unmentioned yet is base damage of your spells. If your base damages are high like those of brand then mpen is much better throughout the game.

Most people take flat ap to have as much early game power so they can use that to try and snowball. Others will have late game scaling runes like mpen scaling mr armor or manaregn or hp et etc and auto snowball in stats if the enemy with their early agme runes doesnt get an advantage early on.

Just ask yourself this do you usually get many kills early on and do you want to make this easier or do you generally play safe or do your games last longer then average and do want to be stronger later on.