Normally you'd think so.
I think Clone Wars just got darker organically because it had to get darker.
I remember thinking that the Crisis on Umbara arc was one of the darkest story lines that I can remember seeing on T.V. because of the shock that a Jedi General would willingly give himself over to the dark side.
Pong Krell: I am no longer naive enough to be a Jedi. A new power is rising. I have foreseen it.
The only thing that was darker was the clone conspiracy arc on season 6 where the clone coldly executes a Jedi during a battle.
Overall the story writing was so strong over the last three years that you could feel the despair and it almost seemed like the writers would stop and realize that they would have to write a very light story arc to balance it out.
I have high hopes for Rebels because that period between ROTS and ANH has never really been properly explored.
I always have that assumption that at least initially Palpatine was incredibly popular because he bought an end to a major war and was removing corruption.
He was the kindly benevolent seat of power who had been hideously attacked and injured by the traitorous jedi.
It wasn't until about what? 30 years later that the kindly Emperor could afford to disband the senate and really put his foot down on the necks of the people.