The most important message of Fauda is that there are no good guys.
Both sides in the show are doing essentially the same thing, one under the pretense of maintaining law and order, the other under the pretense of freedom fighting. However, if you're watching Fauda in order to learn more about Israeli - Palestinian conflict, you're obviously in the wrong place. This is not and never pretends to be a documentary.
Season 1 and Season 2 offer a bleak insight into the lives of the Israeli special forces team trained to infiltrate the Palestinian side in plain clothes. Their job is literally nerve wrecking, both on and off duty.
However, Season 3 takes more of a Hollywood approach, meaning that we're led to believe that a group of highly trained individuals may take on a (small) army and emerge victorious. Therefore you might as well stop watching Fauda after Season 2.
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