Correction. We do not see a fully formed rebellion until ANH. Doesn't mean no rebellion took place at all...
If there were anti-republic planets (seperatist aligned or "neutral") during the clone wars what makes you think all the sudden they would stop putting up a fight after the clone wars? Just because the cowardly leaders of the seperatists were killed doesn't mean the actually people fighting for the cause would be any more cooperative with the republic.
Also, it is said that only a select few in the senate make their unhappiness with palpatine known, because during the clone wars being opposed to palpatines regime is considered treason.
And last but not least, one of the cutscenes from ROTS was an actual scene of padme having the rebllion explained to her by Mon Mothma and Bail Organa and being asked to join.
Take my word for it there was a rebellion