Yes, one point in mpen negates one point in mres, which blocks a certain percent of magical damage, which gives diminishing returns once you go pas a certain point (like, for example, if you have 30 mres you are blocking like 30-40% magical damage, but the more mres you get, the % per point gets smaller and smaller, so if you have 200 mres you are only blocking 75% or so of magical damage). If you have mpen equal to the mres of an enemy champion, then none of your magic damage is being blocked, and having more mpen then an enemy character has mres is a waste of money.
Shen is a tank. One of the best in the game, he gets banned ALOT. He is not the best jungler in the world, he actually has some pretty slow clear times and his ganks arent great, but if you have a strong team that doesnt need ganking, a shen in the jungle works just fine, because once mid/late game hits, he WILL change the course of teamfights. And that is what the mres runes are for, for those teamfights to help make him tankier. If you have any more questions, please let me know XD
Hope this Helped :)
Shen is a tank. One of the best in the game, he gets banned ALOT. He is not the best jungler in the world, he actually has some pretty slow clear times and his ganks arent great, but if you have a strong team that doesnt need ganking, a shen in the jungle works just fine, because once mid/late game hits, he WILL change the course of teamfights. And that is what the mres runes are for, for those teamfights to help make him tankier. If you have any more questions, please let me know XD
Hope this Helped :)

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So if an enemy (NPC or champ) has 0 magic resistance the +MP would not add any bonus damage correct?
Here's the situation I'm faced with... Using Shen and want to try jungling with him, even builds show using +MP runes but from what I can tell from wikia is that NPCs in the jungle have 0 MR... so why wouldn't an AD rune help more for him early game jungling.. Or should it not really matter early game because the MR is for later on vs champs when you gank.
Sorry if my thinking pattern is way off, only been playing for a few weeks..Thanks for any help