I've have the origional MX Master, a couple 2S's, and a 3S (going to order another likely today)...
Function wise, there really isn't any difference between all three versions that I've found, and all of mine still work/charge fine. My reason for upgrading was that my origional MX master started to miss some clicks after years of use/abuse, my 2S's are on my desk and in my bag in use at work daily, and I recently (4 months?) got a 3S from a vendor.
At work I've set users up with probably 20-30 over the years, I've never heard of a battery issue with them and have only replaced one due to a broken charge port.
From the "1" to 2S there was nearly no physical change, a slight color difference, but they nearly doubled the battery life and upgraded the sensor which makes its tracking on any and every surface much better.
From the 2S to 3S the biggest change that took a few days to get used to was how frickin silent it is. My wife nearly killed me a few times clicking away while watching TV with the 2S, the 3S ratcheting scroll and clicks are nearly silent. my biggest gripe would be that they re-arranged the thumb area so back/forward are now in front/behind each other instead of up and down, and they moved the horizontal scroll up a bit to where you almost need to feel for it/intentionally reposition your hand.
That said, I'm kinda in love with the 3S now, and if they could do "something" to fix the issue I have with my pinky getting a divot from how I hold it (every one of my mice has a wear spot about 1.5 inches in from the back right corner from my pinky rubbing) it'd be perfect lol.