yeah, combining characters CAN be useful and maybe the "solution" to some story/plot holes ...
therefore I think the Qui-Gon/Dooku hybrid is the most promising, giving many interesting possibilities, like a returning character (from the dead ?)
and again as for the Jedi as senators/chancelor - I think it is a very "dangerous" idea, why ? - because we, the audience (and possibly many people in the Star Wars Universe) don't like Jedi (as they are shown) ... so turning / bringing a Jedi into a position of power (and Yoda told us, that "real" Jedi don't look for that) is the "box of Pandorra" - antother thing only Sith (dark Jedi) would do ... so if you propose to have a "secret" Jedi in that position ok, THAT could work (if other things fall in place), but the idea of an Roman senate with Jedi in it doesn't (read Yodas teachings!)
some ideas circle around how and who starts the conflict: I think we have a handful of options ... turning the Republic into some kind of "techno union" and making the Federation a pre-(Rebel)Alliance, with many supporters from the alien community - here comes the "radical" idea: make Yoda their leader and Dooku a loyal republic arisctocrat / Jedi / noteworthy persona ...
this would help shift the Republic to Empire later, when at the beginning many (all ?) alien worlds together form the Federation, because of slavery, the massive military force (droid army) and "human/alien rights" in general - leaving behind humans in control of the galactic core (and the key players like Sienar Fleet and Kuat Drive Yards, who build weapons for both Republic and later Empire - maybe some could be "shipped" to the other sides?)
so our "Federation" would need supporting troops, as many farmers and such are not soldiers or trained in combat: enter the clones - could be volunteers or "hired guns", just produce as many to keep the droid forces of the Republic at bay, until the Federation "armies" are ready ...
and this could lead to "capture" the cloning technology (or re-installing it) as a improvement to "keep out the barbarians" - making copies of the best fighters, tacticians, name it who is most valued to lead and support the Republic Army!
Big question still remains: do we want / can have cloned Jedi ?
at the end of the day, it will be brother against brother somehow ... (cue Obi-Wan & Anakin ?)
one possible solution of how to solve the "big conflict" - one other is nearly as we have it, with many tweaks here and there, like a "moving battle/factory planet" and a Republic with a clone army of "commando troops" supporting the enlisted "volunteers"