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I don't mind the liner, unless the edges of it get serrated (Ronhill shorts I'm looking at you).
A good old bit of vaseline works wonders for me, but tight shorts / Tri shorts are my go to for long runs.
Having said that, I haven't run more than 6 miles or more than twice a week since breaking my ankle in December. I have a bit more of a presence nowadays, so maybe I'll have changed my mind when I get a bit more mobile
Or I find cutting out the 'pant' of shorts helps if they have them.
Never really got that liner in running shorts. First thing I do is give them the chop.