Johan was fired because of personal problems between him and the rest of us. We're on different pages musically, it's as simple as that.
The bass is indeed in a more "front" position, but the mix ended up like that and the guitars are quite thin on the record so maybe that's why it's easier to hear. I always regarded the bass as a rhythm instrument so I wasn't over the moon happy about the mix.
Johasn was/is a great player for sure, but he we had some issues with him regarding the musical future of the band + yes, he tried to claim publishing royalties for songs he had no part in writing. I don't think he had bad intentions but it created a awkward situation. I certainly embrace the idea of the other guys writing and I always have, but Johan didn't write any raw music during his time with Opeth. He did however do a stellar job playing the songs and he added some uniqueness that at the time, was unheard of in metal. I still think his solo in the end of "Requiem" is awesome, and his playing impress me to this day.
But, Mendez is better! Of course!
Cheers
Mike