While I can understand the need to wrap up the initial storyline, I think that was ultimately the biggest mistake the show made. It worked in the short-term, they followed up the fall of SD-6 with the search for Sloane and Evil Francine storyline. But beginning in Season 3, that great storyline (Sydney working behind enemy lines to take down SD-6) was gone and just couldn't be replicated again. I rather would have had three seasons focusing on this storyline than the last three we got. Not that I didn't enjoy the show after Season 2 but it was just never the same.
Writing out Will was another mistake although it worked out great for Bradley Cooper. The two times Will returned to the show, it felt like old times again.