And let's not forget the massive programming overlap with Ion.
As for so many of them still having the MNTV-based branding.... well, that's just laziness on their part. But there might be something else. Way back in 2006 when the CW was announced and Fox announced MyNetworkTV in response, stations were rushing to affiliate with one or the other, including changing call letters (sometimes for the first time in decades) -- as if "independent" was a four-letter word.
This was especially surprising as Fox was using MNTV to test a format that was new, at least here in the US: Telenovelas. Dramas that ran five nights a week for thirteen weeks, then ended; 65 episodes and out, replaced by another show of the same length. It didn't go well at all, and the telenovelas were reduced to two nights a week in March 2007 before being eliminated altogether. The switch from network to programming service came in 2009. All those stations that had rushed to affiliate with MNTV and change their call letters and branding probably felt foolish when the whole thing collapsed.
Personally, I think Fox's announcement of the switch to a programming service should have included a request that affiliates move away from their MNTV-based branding. But the aforementioned fear of the word "independent" was likely still at play.