Agreed on all counts, and playing up the Organa/Padme angle is an idea that actually hadn’t occurred to me, but is especially brilliant now that I think about it.
I was originally thinking along the lines of the familial relationship BelatedMedia suggested in his ‘What if the prequels were good series’ but the more I consider deeper an implied romantic tension between Bail and Padme (who would spend a lot of time together while Anakin and Obi Wan are both away fighting the war) the more I like it.
It creates a vessel for the conflict and mistrust plaguing the Republic from within; whereas Anakin and Padme’s relationship is the ultimate symbol of unity between the senate and the Jedi - the public and those who serve them - The hint of a triangle demonstrates the mistrust, doubt and disenchantment the people have for the Jedi, and vice versa, through a very personal relationship.
This theme would additionally tie into the fractious nature of the Clone Wars themselves; the moral dimension of clones fighting natural people which was not an angle presented in the prequels we got, is one that I would love to see played up more. For me the ideal prequels would have gone full tilt into the subject matter of mass cloning and all the moral grey area surrounding; which after years of this conflict dominating society and culminating in war, make Palpatine’s black-and-white leadership (to become dictatorship) all the more appealing to the masses.
Issues like whether the Jedi should take a side at all when it’s clones against people, if they hold all life sacred etc. and what effect (or lack of) cloning has on force potential.
Personally I’d have it that the old Jedi council wishes to stay out of the civil war altogether, while the Republic refuses to grant rights to Clones as those of other living beings, while Dooku Takes leadership of the CIS for them (while also more cynically supporting the industry that wishes to make a business out of cloning etc, but these are extra dimensions).
I’d also make it that cloning a Jedi for example does not necessarily confer force sensitivity, yet a clone of someone who has no force ability may actually have it; the force is in this sense impartial in who it seeks to do its will.
If/When clones of senators start showing up though, the Jedi’s position on clones would also cast them in yet worse favour in the Republic, especially at the behest of Palpatine’s fear-mongering.
These are just some more ideas I’m venting though, and probably quite out there for material for Star Wars.
P.S. Capaldi is a pretty good match for Cushing too, I reckon: 
I think that James Marsters doesn’t have quite a close enough nose, personally, although he’s got the cheekbones:
All 3 are especially notable though for the hard and almost ‘beady’ eyes, sharp jaw and sallow cheeks.