well, before Lucasfilm & Co gave us many books and comics to wrap our minds around, there only were some sources, which held some information on what and why in the GFFA ...
too bad, the PT never laid out what was before the (Star Wars) saga - in ANH "Clone Wars" was enough for starting the new adventure, but if you want a bigger picture/galaxy, then there should be more legend/lore to be told - Episode 1 could have started with a prologue similar to the one from Dune ;-)
the conflict Jedi VS Sith is well documented in books, games and comics - so I find it rather flat to just say: They are the bad guys, because they wear black robes and wield red sabers, and therefore we are enemies.
It is not so much, that I didn't understand, I just heard it as a repeated point of critic: the cause of this conflict isn't clear. (maybe because the virtue of the Jedi isn't that shining and they seem to be all just force-users)
as for the "backstories" there could have been some prelude, though I did like what was told in Episode 3, but that was too late in the game and just a bait anyway ...
ideas for a reason on why Jedi and Sith battle each other for millennia, can be found in many stories (real/fictional) - I stumbled upon "18 days", which is a fine example of what I have in mind - brothers against brothers (or relatives in general), both sides not really evil, but different goals and views.