I'm with you on that one. I certainly did enjoy the fact they were trying to tell a story and attempting a solid direction to go in the whole season. In execution, well... I found it wanting.
There were too many tangents and diversions throughout the season. So much in fact there seemed to me to be more filler material than less plot related content. And yes, the Xindi did seem a bit cliche. It was awfully nice of them to send a prototype to attack a full year ahead of the final version being ready to give Earth time to retaliate though.
They put so much faith in the Sphere Builders, it was almost like a child's belief in Santa Claus. Even when faced with overwhelming evidence, Dolim and the Reptilians just blindly continued on their course for little other reason than they are the bad guy.
Then the way they ended the arc... they end it in an engaging and exciting way where you almost want to cheer Archer as he fights Dolim..... then it's like they got together in a meeting to discuss how they could ruin that in the most facepalming way and came up with the Alien Nazi's.