Color-wise, you're absolutely correct in that. It's also odd that they reverted back after ROTS, with everyone else going to the white suits while the Stormtrooper Commanders re-donning the blue (although it's closer to 501st blue than the Lieutenant blue of the Phase 1). Maybe someone will put on their geek cap and let us know how the blue came about with the 501st.
The 501st was blue because.... George Lucas was experimenting with color and lighting in ROTS, so he made the clones match the scenes they were in pretty well.
For example, on Mustafar, some shocktroopers and Palpatine show up to get Anakin (him having been totally pwned by Obi-Wan at this point), and the lava creates a reddish-orange light all over the place, and the red lava is very prominent in many scenes. To match, the shocktroopers are painted red. Imagine if the shocktroopers had been blue instead, and the orange-ish light on them from the lava made them look purple-ish!
George Lucas just had the colors to match the "mood" he was trying to set for each scene (and sometimes the background colors; the clones on Felucia that kill Aayla Secura have a yellow paintjob, and the background of Felucia is very yellowish with some greens and oranges.)
In the Jedi Temple scene when the 501st is marching up the steps, the night-time gives the environment a blue-ish tint to it, so naturally the clones in that scene are blue.
Also the color and mood has a lot to do with Anakin. The shocktroopers are on red mustafar, red is a very angry color, and Anakin at that point is a very angry person. The Jedi temple scene is blue-ish, and blue is a very cool color (cool as in temperature I mean), and at that point Anakin is being very cold; he's going calmly to go kill the Jedi, even younglings and such.
So as far as I know, the colors of the clones in ROTS has nothing to do with canon end everything to do with George Lucas trying to make colors match the mood of a scene. The Clone Wars series has different colors so the kiddies don't get confused, and also so they will think the clones are pretty or something.