The updates seem GREAT. With these, Riot has really shown that they care about the game. I have been part of many other games, some similar to this, some with had similar balancing issues or meta-issues. And in most games, things like that do not get changed - Riot has, with these new updates, reworked their whole game-mechanic. And that thought alone makes you deserve respect, so good job. I have always been trying to improve games, even though I am just a little member, and in some cases, I even got to have a word in the game-mechanics - so I have rather much experience about such things. So I can say again, you did a great job.
But now, no designer wants praise - they want criticism off the constructive kind~ So lets see what I have to say.
Lets begin with Masteries: First off, i think one Mastery may have a slight tendency to OP: Tenacious it was, if I am correct. These 15% Tenacity + the obligatory Merc Treads give you a whole 50% Tenacity - which I view as rather much. The 15% alone are very strong, and Merc Treads are rather chap and can be gotten right at the beginning. I see the potential of OP-ness there very much.
Another thing with the Masteries:
The new Utility-Tree is great but~ There are too many 3-point masteries, which strikes me as nuisancial - It is hard to customize, as you do not have endlessly many points and usually want to keep your 9 in different masteries. So maybe, you should could some masteries down on being 2-point masteries - maybe with decreased effect, maybe not. It would make customization much easier.
Then the offense Tree... If you have an AP and get the 21 in offense, you face one problems: NO room for real customiztion. Many of the "obligatory points" are 4-point-Masteires, which leave no room for AP's to customize. Maybe you should decrease the number of 4-point masteries and add some new, more interesting masteries(Like Frenzy for the AD's)
The typical AD also does not have much of a choice: But they at least have a lot more variety and, IMO, "stronger" points than AP's have, generally.
Also, the first two tiers of the Offense Tree concern me: In both, you are pretty much "forced" to take 4 points in certain masteries, leaving, again, no room for customization. A similar problem arises, with the need to take the 4-points in the first tier of the defensive tree - you want the veteran scars, and that limits your customization, especially for the first 9 points.
All in all, you should try to add more "situational" or "champ/playstyle-dependant"-masteries and decrease the heavy amount of 4-points masteries in the Offensive tree and 3-point-masteries in teh Utility tree. Also, you could try to bring in customization via the first 9 points, which are often taken, as especially the 9th point is usually a rewarding one.
No to get on the matter of items:
The item changes are great - It allows customizing tailored to your playstyle, which is a great move. However, I noticed that there are rather many shields to come through active abilities... Wouldn't that be a bit much there? Especially an Athene's/Seraph's combination may be powerful, turning even karthus non-squishy. All in all, I also think that there are a tad too many actives overall - that number could reduce a bit, possibly. Sometimes, one just searches for the perfect stat-combination after all.
Also, there are is a item that strikes me as REALLY powerful: Runic Bulwark. It simply screws over AP's. 30 more MR for the team? That is heavy.
And I still see some flaw in terms of itemization: AP's - especially manaless ones - have rather limited choices. Especially in terms of boots: Sorc-Boots are simply the only viable for most AP'S, as they are just powerful. AD's do not have to deal with that problem at all, as the Berserker Greaves are simply no "must" to them. This is something, which could be changed by adding more early-game mpen items, for example.
In any case, the itemization for AP's has increased - yet it is still not that high, as there are too many "musts".
Also, what I want to know: What exactly do you expect from the changes to arpen/mpen in conjuction with the fact, that armor and mr is a lot more costly than it was before?