Truth is, your friend is a flake, which you're totally ok with, and your wife is the one "fixing" things when he flakes out.
That's why she doesn't like him. That's why she's pissed.
He was an acceptable friend to single you but now you're married and your wife wants all your friends to be her friends.
Do what you want. You're entitled to your friendships, but I suspect that as you mature and shift your role to husband and father, his flakyness is going to get old for you as well.
Story:
My husband had these 2 friends he had grown up with, gone to school with, worked with, partied with.
My husband is dense and doesn't always see the obvious.
I personally thought they were flaky opportunistic freeloaders. But I didn't say a bad word about them.
When we were getting married, they were supposed to be groomsmen and they volunteered to DJ as our wedding gift.
I asked my husband if that's what he wanted? He said yes. I said great, but if anything changes he's going to have to deal with it.
The day of the rehearsal dinner and two days before the wedding they decided to go to Mexico.
Hubby wasn't happy because he had no idea what to do.
Our wedding music for a formal wedding was a stereo and CDs and half the groomsmen were missing.
Their friendship ended because hubby saw what I had seen from the beginning and I didn't have to say a word.
If you were the one fixing his flakyness you would eventually get tired of it.