My old bikes have always exhibited the same pattern - round about 2000 miles the shift quality takes a nose-dive. Nothing to do with clutches or suggestibility or personal fallibility or any other BS reason that can be thought up.Yes exactly this. It's 100% oil related. A clutch doesn't magically become correctly adjusted when you change the oil. That's assuming it was out of adjustment in the first place, which I keep on top of.
One of my previous bikes (klx250) used flat tappets instead of roller rocker's, and I had the exact same issues with the oil.
At 8000 miles I checked the valves, and found quite significant wear on top of the cam lobes. Almost like a small wave of metal where the load would come into contact with the valve tappet. So if anything I should maybe be changing it before there is clear friction in the shift lever, and assuming in the rest of the engine too. Though that's not very scientific.
These are bikes with hellish high miles on them and many oil changes over the years, and it's repeatable time and again. In fact, several times over the course of that, I've been forgetful of exactly how many miles are on the current fill only to be reminded by a deterioration in shift feel and realise that, yep, 2K has elapsed (again). Time for an oil change.
The bikes in question are a pair of GS850s and an XJ900, all high mileage and all good runners. Their sump capacites are all around 3L, so it ties in with your observation of the smaller amount of oil in your sump pegging out sooner. In truth, the oil in smaller shared-sump engines takes more of a beating than in larger ones.