One new feature that's come along with the transition is the "association bonus", which allows members of Math Stackexchange --- and other sites that are much further removed from the mission of MO --- to cast votes here immediately without having asked or answered any questions. (As I understand it, these people receive a "bonus" of 100 points which is enough to enfranchise them.)
This, I think, has the potential for a great deal of intentional or unintentional abuse.
For example: One user received an association bonus for participation on Math Stackexchange, where his/her highest voted question begins
In all applications of the theory of sets, all sets under investigation take place in the context of the universal set $U$.
His/her other questions include "What is the difference between an internal category and a subcategory?", "Does every category have a functor?", a request for an explanation of why the statements $A\cup B=B$ and $A\subset B$ are equivalent, and various questions about evaluating the sorts of integrals that pop up in freshman calculus. He/she has never participated in MO in any substantive way (zero questions, zero answers, zero edits, etc.), but has nevertheless cast 28 votes here in the past week, and 46 in the past month. That's a lot of votes, and I think it's a fair guess that they're not terribly well-informed.
A bigger potential problem is that this creates a gateway for unscrupulous users to create new identities, participate on sites where they can earn reputation points simply by posting calculus problems, and then enter MO empowered to vote themselves up. There have certainly been cases of users creating fake identities for this purpose, but at least in the past they needed to ask or answer a real question or two along the way; now that obstacle is removed.
I realize we are not currently overrun by barbarians at the gates, but as a veteran of Usenet, I also believe that eternal vigilance is the price of sustained quality on the Internet --- and I think the association bonus is a significant problem.
Edited to add: Lest anyone think the above example is unique, there's another user, again with no questions or answers on MO --- or at least none that have survived --- who's recently asked on MSE how it's possible to make sense of an ordered pair containing the empty set as a component, who has also recently asked on MSE how the same integral can evaluate to both $g(t)+C$ and $g(t)-g(t_0)$, and who has, thanks to the association bonus, cast 34 votes on MO this month.