I simply do not see any evidence that war damages a Jedi's combat skills. While Force sensitivity heightens the Jedi's reflexes and awareness of their weapon, the actual strength of that connection is not tied to their abilities with a lightsaber. I think this is rather clear also when Yoda and Dooku are having their little force showdown, and realize that they are at an impasse. They then resort to lightsabers, a wholly different arena.
The instructors during these times of war would have most likely had combat experience. As a lot of information regarding particular Jedi is rather sketchy, we can only infer things about how the Jedi were trained, and by whom. Since it is common for soldiers to rotate in and out of combat in order to keep them from burning out, we can only imagine that many Jedi must have done something similar during periods of sustained conflict.
In between these periods of sustained conflict, the Jedi who had fought in the war would have been instructing the newer generations, passing on their practical combat knowledge. Naturally, the First Jedi Purge would have seriously hindered the education of future Jedi. But with someone like the Jedi Exile (an extremely experienced warrior) to begin their training once more, they would have a good starting point. I would also point out that Luke Skywalker was in a very similar position following the Dark Times, and that he was able to train some extremely accomplished duelists.
While speaking of the Jedi Exile, it is true that she developed greater prowess and understanding of the Force while under Kreia's tutelage, she was already a seasoned combatant after the Mandalorian Wars. Also, it is difficult to think of ANY Jedi who would not benefit from her training. (And a good portion of the growth we see in KotOR II is simply the exile relearning old talents, polishing up rusty skills, so to speak).
Yes, Malak, Revan, and Exar Kun were noted duelists who fell to the Dark Side. However, this is likely one part hubris (Anakin Skywalker was also one of the foremost duelists in his time, who fell in large part to his arrogance and thirst for more power). I suppose this ties into the age old question asked by Luke, "Is the Dark Side stronger?" I won't attempt to answer that here, other than to say that Sith tend to be more formidable warriors simply due to their mindset and concentration on combat.
To say that Jaric Kaedan was a lesser duelist because of his focus on one style is a rather arbitrary statement. If anything, his vast experience with combat seems to have taught him that Juyo was the most effective form, leading him to specialize in it (much as Mace Windu did in his own age). Nowhere does it say that he did not learn the other forms, just that he did not spend as much time studying them. There seems to be a concept that "mastering all seven forms" confers a particular advantage on a swordsman, however, there is little evidence to suggest this.
Case in point, Cin Drallig. Vader did not take him by surprise at all, in fact it was the closest thing to a formal duel you could probably ask for. Cin Drallig was alerted to the approaching troops of the 501st Legion, and organized what Jedi were on hand to defend the temple. Vader sought out Cin Drallig and killed his apprentices in front of him before engaging Master Drallig and defeating him handily.
Another point, Master Kenobi. You've acknowledged him as one of the foremost swordsmen of the Jedi order, and yet he specialized in Soresu (with a dash of Ataru thrown in). Likewise, Dooku favored Makashi almost exclusively and was able to go toe to toe with Yoda (a student of every form, but mainly a practitioner of Ataru).
This isn't terribly relevant, but Kit Fisto's feat of "surviving briefly against Sidious" is less a product of his skill with a lightsaber and more due to the fact that Sidious just killed the other two Jedi first. He had a chance to raise his guard while Sidious dispatched his companions, but barely managed one or two parries. There are very few good things to say about his decision to "master" Shii-Cho.
I'm somewhat divided on the subject of the Jedi Master killed by the bounty hunter. You could make the case that the Grand Champion of the Great Hunt is rather an extraordinary case, seeing as he was able to kill an almost absurd number of creatures, characters, and droids. The flat fact of the matter is that the game mechanics make Jedi/Sith and non-Force users perfectly balanced with each other, which is why any scenario comparing the player characters from TOR with other Star Wars characters just gets messy.
And, yes, it's "G-Canon" that Windu defeated Sidious... but it is also perfectly plausible that Sidious WANTED Windu to defeat him. Windu wanted to arrest Sidious, and Sidious wanted to drag out their encounter until Anakin arrived. He needed to make himself look vulnerable and appeal to Anakin's suspicions that the Jedi were planning against Palpatine.
So, to conclude what I'm saying here: Jedi do not necessarily thrive on warfare, but it does hone their combat skills. The idea that the PT Jedi order had "mastered the art of lightsaber combat" is quite farcical. They did not have a fraction of the experience with combat (read: actual lightsaber duels) that the Jedi during the times of the Old Republic did. While the Jedi suffered setbacks during the First Jedi Purge, it seems quite clear that they recovered (much as Luke Skywalker's NJO did) and during the Great Galactic War they certainly got back on their game to fight the Sith.
There is not evidence to suggest that the few notable swordsmen to emerge from the Clone Wars era were exponentially more skilled than their Old Republic Era counterparts. In fact it seems that the body of evidence points in the opposite direction.
P.S. While I welcome Beni's feedback and counterarguments, I'd love to see anyone else weigh in on this discussion as well.