Good idea Reep, I haven't really sat down and looked at the season as a whole yet. I think I'll start by looking at each episode in review...from memory.
"Ambush": Ah yes, the Yoda episode. I liked this episode, the coral planet, the interaction with the clones and the droid combat. Altogether a good solid episode. 5/5
"Rising Malevolence"/"Shadow of Malevolence"/"Destroy Malevolence": The first story arc episode, and not too bad. We get to see Plo Koon and a 'super' ion canon, plus a Y-wing assault. 3/5
"Rookies": Probably the best episode of season 1. The close-up look of the clones was great. Oh, and commando droids! 5/5
"Downfall of a Droid"/"Duel of Droids": A focus on R2, but a little too much Anakin, however I did like the Trandoshan. Overall an okay story arc. 3/5
"Bombad Jedi": A Jar Jar episode...that was actually good. A nice surprise. 4/5
"Cloak of Darkness": The Ahsoka/Luminara episode. I thought this was a good one, Luminara got some face time and there were some good fight scenes with Ventress. 5/5
"Lair of General Grievous": A little darker scenery with Grievous' spooky lair, plus Kit Fisto and his apprentice and some fight scenes with Grievous, altogether made for a neat episode. 4/5
"Dooku Captured"/"Gungan General": Some good and some bad make these two an even mix on the okay side. 3/5
"Jedi Crash"/"Defenders of the Peace": I liked how Aayla Secura turned out and the fight scene over the sky world was awesome. Takei's Sep General was cool, and there were was some nice action in both episodes. 4/5
"Trespass": Definitely one of the stronger episodes. The Talz were really cool and the snow environment turned out really nice. Their was good tension to the story line and a descent focus on the clones. 5/5
"The Hidden Enemy": For a flashback episode, this one was pretty good. Their was a lot of dramatic tension with trying to find the clone traitor, and some descent action with Anakin and Obi-Wan fighting Ventress who was on top of her form. 4/5
"Blue Shadow Virus"/"Mystery of a Thousand Moons": These two were entertaining with a lot of fresh material. There's Jar Jar, Padme, a mad scientist, a virus, Iego, and a zombified looking Ahsoka. My real gripe is that they took the myth out of Iego and didn't play up on Anakin's mention of the Angels on Iego. 3/5
"Storm Over Ryloth"/"Innocents of Ryloth"/"Liberty On Ryloth": The preview of the Ryloth arc looked really awesome, but the episodes themselves fell a little short of the hype, mainly because the previews showed all the action. Of the three, I think Innocents of Ryloth was probably the best, as it seemed a little better than the other two. Mace's episode was so so, and the Ahsoka turmoil episode wasn't all that great either. 3/5
"Hostage Crisis": I was worried on this one. The previews of Cad Bane looked awesome, and I feared a repeat of the Ryloth Trilogy, especially with Ziro's return. However, they pulled it off and made perhaps the second best episode of the season. The Bounty Hunters were just pure awesome, and Cad was the best villain yet. I just hope they don't spoil in season 2. 5/5
So overall I'd say season 1 turned out pretty good for their first run at things. There were some really good episodes and some mediocre ones. The real test will be to see if season two steps it up a notch or whether it's more of the same. Of course as a Star Wars addict I can't complain too much, any Star Wars is better than none at all, but I do love it when they create top notch stuff like Rookies, Hostage Crisis, Ambush, and Trespass.