Let's talk about MR, and AP vs. Magic Pen. [Discussion; Help Please]
Alright, so I've been going over for a very long time and browsing various articles regarding AP, MR, Magic Pen., etc. and I'm having a bit of a quandary.
Lets say that X has 32 MR + 6.7 MR from Seals, which = 38.7 MR at the start of a Match. This is the typical MR resist starting runes for most I've seen unless they decided scaling.
Now Peron Y who is hitting person X with his/her AP respectively:
At max AP in Rune Pages A person can acquire 36.18 AP. If they take Doran's Ring 
which is a typical starting item for Mana casters, they have a starting total of 51.18 AP. If they were to grab the book 
for someone like Akali, it'd be 56.18, but for this theory we're going with the Ring
Also including the +2 AP from Sorcery, 3.67 from Natural Talent, +7 Magic Pen from Piercing Thoughts, and Deathfire Touch which is + 25% of Max AP over 4 seconds (though we're just going to calculate the ending damage to make it easier to calculate).
This = 56.85 AP and +7 Magic Pen.
Note: I'm not including Deathfire's damage above and am instead sticking to Flat AP and Magic Pen.
38.7 MR vs 56.85 AP & 7 Magic pen. Calculation at Level 1.
For this Calculation, I'll use 
whose Q starts at 70 damage + 60% AP which is 34.11 for a total of 104 damage +7 magic pen.
Now, Magic Resistance is an odd calculation at first and I had to do quite a few numbers. To quickly get it out of the way, 38.7 - 7 (magic pen) = 31.7 rounded will be 32.
32 MR and 104 Magic damage.
Now we have to figure out HP into the equation so lets take Lux 
as an Example with doran's ring = 538 HP.
Magic resist uses what's known as "effective health" which is the % of HP-to-MR ratio. 32 MR = 132%. So in this case, Lux with 538 would be
538 + 132% MR = 710 Magic Damage Required to Kill Lux . This = in turn, 7 Q's from Veigar to Kill lux.
Final Calculation, AP runes with 5.31 AP being replaced by 7.8 Magic Pen.
52 rounded AP with 14.8 Magic Pen. Same calculations. 39 MR rounded - 15 rounded Magic Pen = 24 MR.
70 + 31.2 = 101 rounded AP with Q,
538 HP + 124% MR = 667 Magic Damage to Kill Lux
Which STILL = 7 Q's to kill Lux.
This practically amounts to the same thing which is my quandary with this as if Magic Pen and Pure AP aren't much different....