Full mpen vs high ap

It depends on the champion you're playing. If a champion does a lot of magic damage, but does not have great ap scaling (like rumble) then you typically want a lot of magic pen. because he doesn't benefit from tons of ap like other champions might. For a bursty champion (those who have good ap scaling like leblanc) you want high ap because you get more damage than champions with low ratios.

I don't think it's actually possible to have your magic penetration higher than your opponent's magic resist. There are items that give you MAGIC PENETRATION and very few others that give you MAGIC RESIST REDUCTION (Abyssal Sceptor; as well as Fiddlestick's Q, I think?). If your opponent ever has 0 Magic resist, your magic penetration doesn't help, as it has nothing to penetrate. Magic reduction applies before penetration so there's no way your opponent's magic resist will go below 0. Meaning, magic penetration only works if you have something to penetrate. Usually you should have a good balance of magic pen and ap, but usually, if the enemy starts building magic resist (say, if they have >45 mr) magic pen is much better, because it does a lot more damage than flat ap does. If your enemy doesn't build mr at all, it's safe to just build full ap with maybe a void staff or sorc shoes here and there, but considering the tank meta we're currently in, magic penetration is good to have during the mid-late game phase.