I wear softscience on the skiff when my feet hurt or its too hot to stand on the platforms. Simms Currents are decent if you can find them still or Astrals. These two are better for paddlecraft or situations where you need a little more snug fit. All that said, I prefer barefoot so I know there the line is.
Forgot to mention, getting sand in softscience is going to wear them out pretty quick. They are that super soft material inside and sand under your foot acts like sand paper and will chew them up. Wont effect how they feel, but, you will burn through them faster doing that.
I enjoy my pair of Simms Currents. They can be a little snug but provide good arch support and you can feel fly line under foot if you are standing on it. You can also tuck the elastic tightener in the tongue to ensure no fly line snags
I stopped going barefoot many years ago. I currently have both SIMMS currents and Columbia drainmakers. And I put support insoles in them. And after fly fishing from the bow of a skiff for almost 50 years I can honestly say I have never lost a fish because I was standing on my fly line. Never. Probably have lost a shot or two but to me being able to stand comfortably for a long day trumps the small potential of losing a fish.
I should add though that I much prefer to use a stripping basket too so having a fly line laying around is much less an issue.
I have used both Simms currents and challenger shoes but trying a pair of new balance running shoes that are super light and comfortable that have very little tread to hold sand/grime and they are non marking and white bottom.
Better than flip flops as they don't fall off if you have to leave the boat even in mud. Open air so no stinky shoes. Self draining. Tread suitable for hiking and non-marking. Tread lasts hundreds of miles. I have some that are 12+ years old and still have half a tread. Sole that is truly protective against anything a person might step on in the water or on the boat. Highly adjustable and available in wide widths. Nothing between the toes (which I personally dislike). I also like the fact that as my feet swell and shrink nothing pinches or gets too loose.
Pretty much the only thing I wear outside of formal events.