Question for those with more than one set of wheels

I have three hand built sets (thanks DCR Wheels) each has its own cassette and they get swapped between bikes as needed

If a person is using two sets of wheels for one bike that usually means they have training wheelset and a racing wheelset, each set would have a different gear profile.  While changing the cassette isn't a big deal (plus cleaning your hands afterwards) but why bother doing it since the cassettes aren't all that much money anyways?  Also why put twice the wear on one cassette.

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Done this for several years to make it easy have cassettes on both wheelsets run disks and currently get away with not resetting calipers despite different hubs
To avoid issues around chainwear and cassette wear i do regularly use a chain checker and retire chains promptly
Never had an issue with limit screws sometimes a quarter turn on inline adjuster to get indexing correct
Works well for me mainly ride mixed gravel on 35mm tyres but if going on a 100% road ride or some event that dictates riding a bit faster will fit the wheels with more trad roadie tyres
N-1 though

Cassette on each wheelset, will save you the most amount of time at the time when you need to save that time (i.e., when you wake up to go for a ride) if you don't have time to set everything up the evening before. (Or you have better things to do with your time.) Don't worry too much about differential wear, chain will see to that. Or if you do, swap the cassettes between the wheels at periodic intervals (when you have time).  Change chain every 3 months.

Across two bikes I have a total of 4 wheelsets on the go at the moment, with 4 different cassettes (not always the same on each wheel). 

The reason is a combination of old as a turbo wheel,  basic (winter) and two different rim depths for fair  weather riding.

All are compatible with each other, none has massively more milage than any other, no jumping/ skipping etc. You just need to swap over the cominations quite regularly to ensure they wear with your chain.

Introducing a brand new cassette or chain into the system after 000's of miles will invariably cause some problems however. 

I'd be more worried about the difference in limits between wheels - just changed some over and if I'd used hte first wheels with the second wheels limits, the mech would've been in the sprockets. And vice versa for the frame.

I run two sets, one set aluminium and the second set carbon with aluminium breaking rims. Means brake pads don’t need changing, just adjusting for different wheel widths.

I keep separate cassettes on each, just for convenience.

My main issue is between swapping carbon wheels and alloy wheels so time is irrelevant as you have to swap out pads and I only run three road bikes with gears anyway, having said that I buy a wheelset a cassette and a chain, if I'm changing wheels for different uses I'll tend to be wanting a different ratio any way so having a chain cut to the right length and Quicklink makes it much easier. I keep the chain in a poly bag in the myriad wheelbags in the bike room, makes it much simpler for me, You know each chain has done the same miles as the cassette.

MTB's are much easier Hope hubs, 160mm rotors, S-Works tyres and Various Chris King King Sprockets, that's just a swap out depending on the conditions of the race!

Unless your kit is really high end and you're doing a ton of miles then just go with the cassette on wheels same chain advice.

If you are doing a lot of miles or leaving the wheels on for a decently long period of time consider swapping chains too afterall a chain takes similar time to remove fit as it does a cassette so swings and roundabouts in that respect.

with the right tools, swapping the cassette over takes about 3 minutes

I ran two wheelsets last winter. Both had cassettes installed (same ratios and manufacturer) and I used the same chain. The whole drivetrain was new components at the start so the only item that wore at a different rate was the cassette. Didn't have any issues with shifting performance when swapping to my wet weather wheels from my best wheels. Probably 80/20 usage between the two wheelsets over the winter. Depending on tolerances you might need a small tweak on the rear mech barrel adjuster to sort out indexing but I never did. Obviously important to get the wheel centred in the dropouts - mine was a disc braked bike with a QR at the rear rather than thru-axle but I didn't have any issues.

I think if you abuse your chain, or the cassettes don't match in terms of spec of age you'll get issues, but these are overstated in real world use.

Each of my rear wheelsets has its own cassette. I use the same chain on both and follow my normal routine chain maintenance.