I think the maneuverability difference in the two as described on Gonzo's website is close enough to be classified as statistically insignificant, as they are probably within the accuracy tolerance for the flight tests used to compile that data, i.e. they are practically identical in that regard...
IRL, the D-40 had dive flaps (added on the D-30 block), the K-14 gunsite, the new tail warning radar, rocket stubs, and the dorsal fin. I'm not sure what model engine came on what model Jug in real life, but it appears that HTC modelled the D-25 with the R-2800-63 (2300HP at WEP) and the D-40 with the R-2800-59 (2535HP at WEP). I'm guessing that is the difference in climb rates between the two. I may have transposed my Double Wasp model numbers there.
Strangely enough, I find that the D-25 feels more spritely than the D-40, and don't seem to notice the difference in WEP ratings in combat (although it would seem that 235HP difference should be extremely noticeable). Could be I'm just not observant enough to notice the difference.