When I first got the WoP3 pack, I asked myself the same question. Here is what I found:
http://ww2fighters.org/forums/index.php?showtopic=3803 (Links to WoP2 screenshots are embedded within for comparison).
This is by no means an exhaustive comparison. The WoP3 was built with the AccuSim expansion in mind, and AccuSim is what really pushes the WoP 3 version way out ahead of its predecessors (and IMO, ahead of all FSX single engined prop fighters currently available, including the RealAir Spitfires, the *SPAM* P-51B/C and the Real Flight Simulations F6F Hellcat). But if you aren't really interested in AccuSim or working turbo systems, etc., the WoP3 version is still an improvement over the WoP2 version in several aspects. The product's preview videos showcase the more realistic metal skins and cockpit shadowing, for example, but the cockpit is also much improved. Bottom line for me, the WoP3 version is so much better a flying experience that I was comfortable with completely deleting the WoP2 Thunderbolt from my FSX folder.

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I like Thunderbolts! (Link to MySpace tribute page)
120th Fighter Wing, Montana Air National Guard