Freeform probably. I don't know Saga, but if it's like the rest of D20 i'll probably loathe it.
That said I am willing to learn most other mechanic systems.
And Unisystem Lite can probably be adapted easily if you guys want to use a system. I love Uni-Lite's versatility. I'd probably enjoy designing Jedi powers for Unisystem.
But freeform's probably the fastest, easiest option.
As for how the Kai fight the Jedi...
The founder of the Kai has dedicated extensive years and resources to researching ways to balance out the common man's chances against the Jedi/Sith. The more elaborate or potent techniques and resources are reserved for the more Elite, high ranking Kai. He has dedicated many years, and enough credits to purchase his own vacation planet on researching Jedi/Sith lore, and amassing weapons and resources to outfit his recruits. He also salvaged an Old Republic-era Starship(a Phantom-class ship, if you're familiar with the new Old Republic MMO). His datadroids were able to recover 30% of the vessel's computer records which contained...amongst other things...the formula for Cortosis-Weave.
He also has access to a small supply of Phrik metal from a mostly tapped out mine. His personal guard-droid, a salvaged Magnaguard, is completely armored in Phrik, and still has all it's old memories of all the Jedi it fought and killed in the Clone Wars, so it also helps in teaching various techniques for fighting and beating Jedi to Kai recruits. A large part of his Phrik supply went into that endeavor, but he has enough leftover to pass out some nice bonus goodies to a handful of his best warriors.
For rank and file Kai, he trains them in basic-to-moderate Teras Kasi techniques to give them at least rudimentary techniques to shield themselves against at least some Force Powers. He also has them equipped with weapons and strategy lessons specific to Jedi/Sith. No lightsaber can deflect a flamthrower, or Sonic blaster, or Sonic/Flash/Thermal Grenades(Which can be set to go off immediately if their trajectory abruptly changes...as if they just got force-pushed for example). They generally don't do too well with Slugthrowing Scatterguns(shotguns) either. Simply using weapons that make it impossible for a lightsaber to bounce your own shot back in your face goes a long way toward increasing the random's mook's survival odds in a Jedi encounter. Other strategies are also used. His rank and file soldiers avoid direct engagements when possible, since inert traps tend to fly under Jedi radar alot more easily than snipers and highly complex trap mechanisms do.
Those who show more promise in basic training receive more advanced Teras Kasi training, and Echani training to boot, giving them a combat-precognition that rivals Force Combat-Precog. Arguably it's even better. Jedi Combat Precog is pretty hit and miss. Sometimes it works. Sometimes it doesn't(as countless Jedi learned the hard way when Order 66 came down) . Echani Body-reading works much more reliably and consistantly, at least as long as you can see your foe.
The Master of the Kai has also devised his own fighting technique that can be used barehanded, or with Staves/Batons. With it you can strike various pressure points that can temporarily disable limbs and/or force powers(If you ever watch Avatar the Last Airbender, thing of Ty Lee's ability to temporarily render both limbs, AND Bending powers useless).
The Kai Master also has intimate knowledge of the Jedi and Sith lightsaber forms(mostly from having spent years fighting and observing those forms, and also from various holocrons he has aquired through research and archeological endeavors he has funded...or personally spearheaded in some instances), and trains his best warriors in how to recognize and identify the Form being used, and to know it's strengths and weaknesses.
As for the Master of the Kai himself, he has a personal equalizing advantage in any fight with a Forceweilder. A natural(Well, not 'natural', but that's a whole other story. And a long one) aura that functions much like a Ysalamir aura(Basically canceling out Force-powers in in a ten foot radius/bubble around himself). In addition to ongoing genetic and cloning experiments to find a way to duplicate that ability in others, he has a small number of actual Ysalamirs for special occasions. The little bastards are proving difficult to breed or clone, but occasionally he'll loan one out to an operative for a special assignment.
Vornskyr on the other hand have proven MUCH easier to breed and clone, and it's fairly common for even rank and file Kai teams to have a few Vornskyr hounds ready to stalk and hunt those tasty Jedi and Sith. Sometimes if they know they're about to face a large number of Jedi/Sith, or a handful of really strong ones they'll unleash a dozen Vornskyr on them first to soften them up.
While the Kai Master has proven unable to duplicate his "Anti-Force" ability in others, an alchemical concoction brewed from his blood has proven effective at permanently severing Force-Sensitives from the Force without killing them. Well for it to work permanenetly it has to be a treatment process involving a heavy transfusion of the compound. A common practice amongst Kai before engaging a Jedi or Sith in battle will be to make them a one time offer to submit to having their connection to the force severed or face the consequences of resistance.
Expanded Universe Alumni will no doubt conclude many Jedi have overcome many of these methods and techniques...but they overcame them on a rather small scale...and usually the Jedi who overcome these techniques are the hotshot, elite ones. The Skywalkers, Solos, and Katarns of the universe. And usually the trick in question is being used singularly. Overcoming a pack of Vornskyr is one thing....overcoming a pack of Vornskyr being commanded by a Cortosis-Armored Teras Kasi master with sonic blasters is another matter entirely.