Marksman
Why?
The only other options in the offense tree are AP or hybrid based. Some of the other abilities may benefit champions like Corki or Ezreal, but the points in this tree seem most cost efficient for AD carry. Also, I guess it could be personal preference, but I've always thrown points into CDR versus attack speed. You might want to swap the two if you're playing someone like Graves with a sluggish last hitting animation and you think you'll notice a difference.
Unlike Season 3, the Defensive Tree doesn't give a huge advantage in lane for just 9 points. Overall, the points in utility will help your lane more, especially the enhanced potions. If you want, you can sacrifice Culinary Master for Runic Affinity if you prefer to hold onto red/blue buff longer.
Jungler
(all abilities described assuming you're a melee jungler)
Why?
Utility jungling received a buff in Season 4 because the utility tree has a ton to offer. While going deep in the defensive tree has its merits, it doesn't justify the 21 point investment because mostly everything in the tree will be capable of being bought with gold. You'll be making more gold in Season 4 jungle as well as with these utility choices, which also offer valuable goodies that can't be bought with gold. With 21 points in utility, you'll also be able to zoom around the map and to other lanes faster due to the massive amount of move speed you get, especially out of combat.
?Singed
Why?
(I like Singed a lot so he gets his own page.) This was actually really tough to theorycraft because 21 utility seemed extremely tempting. However, weighing the two against each other, the defense tree had more to offer and makes Singed's laning much less painful. One very important thing to note is that Strength of Spirit was moved higher up the tree in Season 4, so even without heavy investment into utility, you'll be rewarded for your mana. I only took the first two regen points in the defensive tree because the CC reduction and crit damage reduction are too important.
The last few points of the Defense tree are hard to decide on, but ultimately, I feel Tenacious is a necessary investment. In a full teamfight, it's 20 armor and 10 MR just from one mastery. That's amazing. It's possible to have taken 2 points invested into biscuits/potions out of utility and put more points in the defensive tree or one point in Butcher, but ultimately, you're going to be chugging potions a lot as Singed, and I'm assuming the mastery will also work on Crystalline Flask. (Also, he's a chemist.)
Last, but not least, I don't see any point in investing more than a very small (if any) amount of points in Offensive since you don't acquire penetration until very deeply invested into the tree.
?Bruiser Top
Why?
Bruisers are a little hard to spec compared to Season 3, but there's no point in putting 9 in offense in my opinion. I calculated the best point efficiency per additional damage and sustain in offensive and put the points in there. It was possible to invest more into utility, but ultimately the end points of the defensive tree are extremely powerful for someone in the middle of the fray. At the same time, I saw no point for most bruisers to invest more than 21 points into Defense, so I put the last 4 into utility, with 3 of the points being in move speed.
The 4th utility point could have gone into Phasewalker, but I decided that as a top laner, it's more important to have cast range on your trinkets, especially if you're going to be getting camped by the enemy jungler. The extra safety cetainly helps. While this works for most bruisers, I think it'd be justifiable to take some points out of Utility and Offense to work towards Second Wind in the defensive tree for the additional healing at low health. This is probably a good option for someone like Jax or Vladimir.
Support
Why?
This one is pretty much a no brainer since Riot clearly designed this tree to help supports stay relevant late game. You take the sustain and damage reduction points in defense and throw the rest into utility where you make gold, get more experience, and move faster around the map. I honestly feel like you're gimping yourself if you don't pigeonhole yourself into this build.
?Offensive AP / Hybrid
Why?
Despite how much time I spent theorycrafting, AP mids are the most awkward to build for, so I'll have two pages. In this one, hybrids and champions that auto attack inbetween spells benefit most. You get all the + magic damage goodies while also having very good auto attack harass. Hybrids really thrive here since you get double penetration going this route. If you're like me and you auto attack a lot as a mid laner, you'll appreciate this spec.
I think this will be strong on standard AP's, but characters like Teemo, Kennen, Sion, Kayle, etc will benefit the most. If you're playing a less sustained/poke AP and relying on one shotting someone, it's probably best to take the points out of the hybrid abilities and put more into executioner.
?Balanced AP
Why?
This is the best balance I could find for AP, despite how hard I wanted to make 9/0/21 work (or any variation with more than 9 in utility). It turns out that most of the right-aligned masteries in Offense are way too important for mages, and going without any % magic pen is brutal. The only thing you should really be switching around is maybe one point in offensive CDR for Double-Edged Sword, though it's a bit risky, especially if you end up getting camped.
As a mid laner, I rank having buff duration higher than the upgrade to biscuit because of the strength of blue buff even after the CDR nerf. This is obviously up to preference, but I feel you have a lot more to gain from having more lane control for longer.
Why Recovery over Enchanted Armor?
It's a matter of preference, but I'd rather have the regen in lane than the bonus MR/armor later. Armor and Magic Resist have diminishing returns the more points you have, and 2 hp5 offers a free health potion after about 5 minutes in lane roughly. On top of Doran's shield with someone like Singed or Rejuv Beads on someone like Riven, I feel the synergy is strong enough to use these points.
Why don't you ever take Runic Shield?
Honestly, I feel it's not as great as it sounds. I feel more damage will be mitigated from when you are alive to when you die next from the extra point in Tenacious, especially when it comes to a 1v2 or 2v2 scenario top lane or in the jungle. The ability would be awesome if it wasn't near the bottom of the tree, but every point in Tenacious is just so powerful.
Thanks for reading and don't forget to check out Riot's mastery calculator so you can do a bit of theorycrafting on your own! Let me know what you think is best in the comments.