Whether or not it's meant as a shot at him doesn't matter, John feels it as if it were. Since Finch disappeared, he's done nothing at all to move this team forward and he understands why they looked to him to get that done, he knows he'd always looked like Finch's partner more than his employee, but that's not how it had been. They'd been friends, of course, but when it came to work, Finch was the leader.

John was just his loaded gun.

"I was thinking about you," he explains instead of focusing on his lack of initiative. "Wondering if you might know anyone who would be as good with computers as Harold could be." Pausing, he reconsiders that before continuing. "Someone who might be half as good would do. I know Harold was exceptional."