The best and worst of Season 3 Masteries:
Offense - Destruction: In season 2 masteries there was a +10 damage to turrets. This was useful in early game dominating team compositions. The 10 damage was added after armor reduction, effectively being true damage to turrets, albeit little. The new mastery you need 200 damage for the crossover point for that a turret with 160 armor BEFORE armor calcuations. It does so little damage early game and is not even close to worth it later.
Defense - Safeguard: The other tower mastery. 5% damage reduction to turrets is not going to be the reason you won. Another trap mastery just like the trap item Ohmwrecker that can easily be fixed through good tower juggling and team comp.
Defense - Defender: +1 armor/MR for each nearby enemy champion. While not bad, it almost doesn't make the cut for "good" masteries. Absolutely amazing in ARAM and level 1 teamfights, specifically for 1 mastery point. It's worth atleast the same value of T2 masteries, and you can't really go wrong with one point in it.
Defense - Legendary Armor: This mastery is pretty bad. It only scales off bonus armor/MR. So it may be good on those champions with tank steroids such as Leona, Galio, Rammus, Jax, but it is really not worth the three mastery points that could be put into Tenacity and %hp.
Defense - Good Hands: While not a bad mastery, it is saying that you intend to die. Which is perfectly acceptable in this game. In ARAM it is particularly powerful, but in a real game it may only apply to close games. 4-6 seconds off respawn is when it is at an "optimal" power level. Way better than it's previous 3-point incarnation of Season 2.
Defense - Reinforced Armor: -10% Critical Strike damage. For one point I suppose it's okay, but the people who take this would be selective to the enemy team if they have 2 ADCs like Kayle in top lane, any ADC bot lane--or maybe even the rare support Ashe. It reduces crits to 180% damage, but after Infinity Edge you are still taking 225% damage from crits. Probably more considering the Lethality mastery. Once again, good but not worth the point you could be putting into other masteries making it subpar.
Defense - Honor Guard: to be honest this mastery is meh. But since you are already this deep, it's okay when compared to it's 3-point Season 2 version.
Utility - Improved Recall: I can't believe they kept this mastery. It's a waste of a mastery point and will totally not be the reason you won the game. Odds are you are probably spending 800% more time in the shop than this mastery will save you if you take it.
Utility - Scout: I'm glad they did something to try and fix it from last season but it is still not worth the point.
Utility - Expanded Mind: It no longer gives +energy for energy champions and is no longer a prerequisite for Meditation. Not worth the points.
Utility - Strength of Spirit: It's back, but still too deep in the tree to consider taking over any other decent mastery. Maybe if you were expecting a siege game in ARAM it would be good.
The Best: (in short, everything else--but the BEST of the best:)
Offense - Penetration: Obviously better with the %pen coming before flat now.
Offense - Spellsword: helps in last hitting when combined with Brute Force. Mid game when you have 300-400+ AP, putting 3 auto attacks in a teamfight will raise your damage output by 45-60+, possibly more. That could be the difference in teamfights.
Offense - Havoc: Still pretty meh. Will not matter on ADCs as much but on APs it will matter a lot considering how high base damages are.
Offense - Archmage vs Mental Force - Switching points between these two if you want. The crossover point-by-point is 200 AP.
Defense - Unyielding + Block: Particularly annoying how much damage this thing will prevent. It prevents it after armor/MR making it even stronger and then it stops spellsword making it EVEN STRONGER. This combined with Doran's Shield will be amazing in top lane tanks.
Defense - Vertan's Scars: No need to say anything about this. It has been the #1 contender for best mastery since preseason 1. It's extremely cost efficient and you don't have to delve deep to get it.
Defense - Tenacious + Juggernaut: Easily one of the better masteries. Consider maxing both of these out. Even tenacious against cc-light teams.
Utility - Mastermind: Absolutely absurd that this came back from season 1+2 and so early in the tree. It's three points, though but it's still worth it.
Utility - Biscuiteer + Explorer: Could make and break level 1 teamfights. Super potion + 60 second ward when it matters.
Utility - Pickpocket: Considering that the average good mastery point is worth about 40g in in-game stats, YES THIS IS TOTALLY WORTH TAKING. AP Mids should already considering going deep into the utility tree for 21 points, sustain, ward, biscuit and this mastery.
Utility - Nimbleness: With all the movespeed getting removed and base movespeed increases, this got a lot stronger. AP Mids benefit the most from this.
Well that's all I have for this article. I may write another article talking about which of the new items are must-haves. (Hint: Sightstone is OP)