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.
Nothing about the Xindi's actions really made much sense.
1) Why exactly did they attack Earth the first time anyway? We are told during the course of the season that it was meant to be a test. Who tests a weapon on the ACTUAL TARGET. Furthermore the test theory makes less sense when there is an entire episode called PROVING GROUND featuring...A TEST SITE? So...why did they attack Earth again?
2) What was the point of Carpenter Street? If the Xindi had access to time travel why bother creating a plague? Why not just conquer the planet? Speaking of which...what was the point of the biological weapon? The whole point of the season was that they were developing a planet killer.
3) We learn later in the season that the Xindi do all of this work and killing on the word of the Sphere builders with NO PROOF. Lets be clear here, the Sphere Builders tell the Xindi that a race that up to that point they had never encountered was going to destroy a home world that they don't yet have centuries in the future...and the Xindi decide to go all genocidal without asking for ANY evidence

Even after the attack on Earth, Starfleet and the Vulcans were having a hard time believing the story and they actually had evidence. This just made the Xindi look stupid.
4) On several occasions during the course of the season the Xindi have ample opportunity to destroy Enterprise....yet they don't. Why exactly did they let it roam around freely for so long. Hell in Azati Prime, they have Enterprise on its knees...why exactly didn't they destroy it? Remember, these are people that are about to commit genocide on a grand scale. What were they leaving Enterprise around for?
On top of the peculiar actions of the Xindi, we are also left to wonder why Earth would want to have ANYTHING to do with the Vulcans after this fiasco? Let be clear, the Xindi launch an unprovoked attack on Earth and the Vulcans...do nothing. In fact they do everything in their power to prevent Enterprise for figuring out what's going on. One wonders why Earth would want to have any sort of relationship with the Vulcans after that. (and Twilight makes the Vulcans look even worse since they apparently stood by and let the Xindi systematically exterminate the human race and then refused to aid the refugees).