I think the reasons are mostly historical, people use what has been working well for them. I find vitronectin easier to work with, easier to control colony size with when using EDTA-based passaging. I haven't seen reports of vitronectin ever being inferior to Matrigel but if there are any, I'd love to read them. Plus it's been a while since it was commercialized for PSC culture and the adoption is increasing.

I chose to stick to Geltrex over vitronectin simply because I found no significant difference in results and the former is cheaper.

I've used both matrigel and vitronectin for culturing iPS and ES cells respectively. With matrigel I found that it's a bit more forgiving for attachment of cells so that could be a reason why others still use it. Currently I use vitronectin because we need a highly defined and controlled coating protein. But both work perfectly fine IMO.