The real reason I think they weighted so long to arrest Winston.
Near the beginning of the book, there is this passage:
"Winston’s greatest pleasure in life was in his work. Most of it was a tedious routine, but included in it there were also jobs so difficult and intricate that you could lose yourself in them as in the depths of a mathematical problem—delicate pieces of forgery in which you had nothing to guide you except your knowledge of the principles of Ingsoc and your estimate of what the Party wanted you to say."
Now consider O'Brien's work. Most of it deals with tedious people like Syme, who will never consider the deeper implications of what the Party does, but are nevertheless too intelligent to keep around. Doubtless, there are many Symes around that speak a little too plainly and need to be removed.
But Winston? He is the difficult and intricate work that O'Brien is entrusted with. Unlike the others, Winston analyzes the philosophical implications of what the Party is doing: how lies are reshaped into truth, how a an uprising of the proles is required, how thought is being constricted and history erased. Most people don't care about this; Julia only gets slightly philosophical because of Winston, but is only really "a rebel from the waist downwards".
"In a way, the world-view of the Party imposed itself most successfully on people incapable of understanding it. They could be made to accept the most flagrant violations of reality, because they never fully grasped the enormity of what was demanded of them, and were not sufficiently interested in public events to notice what was happening. By lack of understanding they remained sane. They simply swallowed everything, and what they swallowed did them no harm, because it left no residue behind, just as a grain of corn will pass undigested through the body of a bird."
In a way, I think this is the reason why she was able to fly under the radar for so long; she simply didn't care about overthrowing the Party until Winston. But Winston stuck out and was identifiable by O'Brien and by Julia, only that O'Brien recognized what he would become first.
It is this philosophical tendency that the Party wants to watch grow and reach its zenith, because there is no better way to test their methods then by brainwashing a philosopher at the prime of their rebellion–no better way to cull a population of its would-be revolutionary thinkers than by predicting, crushing and "debunking" their arguments just as they grow into them.