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You're right; the plugs should be good, but 30k miles is quite a few. I hate to send you down the wrong track, but it's still very possible that it may just be plugs.
Does it behave this way in neutral, i.e., when there's no load on the engine?
I have no idea what you're talking about when you say it behaves like a "cold engine." My car is slightly lethargic when cold, but this seems mostly due to shifting behavior. I really have no "cold engine" behavior to speak of.
Another possibility, though somewhat outlandish, is that in a particular gear (second maybe) the clutches in the transmission are working against each other. I'm not sure how likely this is, but I reckon it's very possible. I'd have to study up on this to figure out how that would work. As soobiesvx93 suggests, having your torque converter lock up at the wrong time would do the trick. Pull the transmission codes too if you haven't already.
You might try manually shifting the car when it does this. Just moving the shifter to third for a split second will completely disable the torque converter lock up, and will also momentarily release the overrunning clutch. Anything you can do to get the transmission to hiccup might help overrule an engine-related problem. ...although I think you're probably already on the right track.
The fuel filter may be plugged. Some systems have a pressure relief valve that will release when demand for pressure is high enough. Fuel filter problems have a tendency to exhibit strange symptoms.
svxistentialist mentioned vacuum leaks. That a very good point. Normally they affect the engine's idle, but this isn't always the case. It is however very common for vacuum leaks to "go away" at higher engine speeds, as they don't leak as much under low vacuum and bleed proportionately less air at those speeds anyway.
A few more off hand ideas: A hydraulic lifter may not be pumping up at low revs. A burned valve may reduce pressure enough to prevent combustion. Your engine may have a loose connection that comes and goes as the engine rocks back and forth inside the engine bay under torque - which there isn't enough of below 2000 RPM.
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