The Clone Wars Refocused Cuts all of the Filler

Personally, I think the best way to watch The Clone Wars as a whole is to watch The Clone Wars: Refocused. This is a fan edit by Eddie Dean that brings all the Clone Wars content into a nice whole and removes a lot of filler. If you do watch this way, I recommend not watching the extra episodes if you want to avoid any filler. Eddie has a great spreadsheet that has a viewing order and what to watch based on your preferences though. I also recommend, watching his coda for rebels as that show has a lot of filler and I personally can't recommend it has a whole.