What a lovely little pothos. Those are adventitious roots. Do not mess with this plant, don't cut the leaves off or those roots. It is beautiful. To make a THICKER denser plant the best way to do that is to pinch off the apical or terminal roots. I just do not see any problem with this guy whatsoever.
I am glad you've decided to up pot this guy. Needs it amazingly tough plant. Do not get a pot larger than 6" in diameter. Perhaps in a year you'll need to up pot this guy again but do not go too large too quickly.
Use bagged sterilized potting soil. Do not use garden soil. No rock or gravel at the bottom of the soil above the drainage hole. Just bagged potting soil. Water well and allow the soil to dry before watering again. This plant would also love a 'shower' once every couple of months. Put in shower, turn cold water on and allow to 'rain', cleaning off the leaves and soaking the soil. Turn off water and allow to drain. Shake the plant a bit before putting it back in its normal place.
You do know that this is a vine, not a shrub type plant, yes? And one of the best plants for indoors. During the summer this guy and any indoor plant could use some outdoor time on a covered porch. Helps produce more food to be stored in the roots for winter and makes indoor plants last longer and thrive.
A little osmocote twice per year and you are good. No need to spray or prune at all. New foliage is always lighter and yellowish. When was the last time this plant had fertilizer? Osmocote 14-14-14 extended release fertilizer, half the label dose twice a year is all this guy needs...as well as bagged sterilized potting soil. Water well, then allow to dry before watering again. A hanging pot might be a good idea as this plant keeps on lengthening as a vine.