I think the issue folks had came down to freedom of thought. With just the first movie, so much was left to our minds... the war between machine and man, the nature of reality, everything. So everyone had ideas. Everyone WANTED to put forth ideas. The comics, the AniMatrix, everything this concept birthed came about because we wanted to know more. And like any good film, we imagined because of it. We wondered about the nature of Zion. About the nature of the machines. About how someone/thing like Smith could exhibit a very clear-cut emotion... unbridled rage, spite, and hatred. Even folks who hated it could find things to talk about in it.
The biggest no-no in a magic act is to show how it's done... to ruin the magic and the wonderful questions magic produces. And that's what the sequels did. They revealed what the Brothers viewed as being The Answers. And for a lot of folks, the truth didn't live up to what they had in their minds.
Now, are they BAD movies? Oh, hell no. No no no. Bad movies are the works of Ed Wood, or Coleman Francis. Bad movies are the ones where nothing entertaining occurs on purpose; the deep film you laugh at, or the dramatic dialogue that envokes childish chuckles, or the comedy that makes you long for the sweet release of death. What they were was pulling back the curtain and revealing the Wizard of Oz for what he really was. And the truth just fell short for a lot of folks.
That said, I loved the whole trillogy. I loved the final fight, I loved the mechs, I even enjoyed the frakking rave. It didn't do everything I hoped it'd do, but it entertained me and interested me. And at the end of the day, that's all I wanted. Keannu Reeves was not going to be answering the question of reality and the meaning of life. He was always going to recite lines, kung fu fight, and shoot guns in slo-motion. And I never asked more of him than that.
That said, the video games blew total chunks.