As I observed the other day (offline), "It took 3 seasons for Patrick Jane to have a conversation with Red John. It took Sherlock Holmes a single season." :)
When the series Elementary first mentioned Moriarty, and for a while after that, I thought perhaps it was Sherlock's father. {M.}{tis a good reason to remain distant, isn't it - so your son doesn't know you're a criminal mastermind}
...later, towards the end of the first season, I began to wonder if, perhaps, Moriarty might be Watson's father.
...but in the end, it turned out to be:
The Woman.
The scriptwriters did a good job of unifying the characters...even in the Canon, Irene had her own plans and goals both near- and long-term.
{and with even the moments of intimacy and tenderness between them, focusing almost more on the intellectual aspects, was at least a concession to the first page of A Scandal in Bohemia}
What was that comment Mr. Tennant made about the 3rd Doctor's Master in an interview? Ah yes, that he makes you think that maybe this time, the Doctor won't win.
...and that's what Irene's Moriarty made me think. (and, on more than one level, she did win - in that she accomplished the goals she had set out to complete)
{though I'm still wondering where all the blood came from}
But the biggest danger is one we have not yet seen.
Even if Moriarty remains in police custody {not a certainty, given her resources}, what will become of the spider's web? will it break apart into a hundred smaller webs, or will her lieutenants and captains and generals fight for the position of being the new spider of Moriarty's web?
Things will only get hairier. And more interesting.