It waited until the 11th hour because it didn't know who was actually leading the humans until the humans won.I think for me the crux of it is that Skynet sent back a Terminator, and then Judgement Day happened. I don't see any reason why it would wait until the 11th hour to start going after the future resistance leaders unless they're just the secondary objective, and the primary mission is somehow helping it's past self. Maybe the full data and schematics on time-travel so it can start firing off Terminators into the past much earlier. Maybe it's a full copy of future Skynet. Maybe it's just a tactical data packet to give it a head-start on future engagements. I mean it can pick any time it wants to target resistance leaders, whatever the writers intended; that it chose Judgement Day itself is far too much of a coincidence to ignore.
In a weird way, Skynet has become a sort of temporal von neumann machine, only it's self-replicating fourth dimensionally instead of three. Though one has to wonder why with all of it's capabilities, Skynet doesn't just bugger off into deep space. What's so great about Earth that it feels the need to stick around?