If at the end of the day I'm going to replace TouchWiz/Sense crap with better things on the Play Store anyway, why should I care that TouchWiz has a few better crap apps than stock along with many other useless bloatware gimmicks that do nothing except bog down the system?
Calendar: I'm replacing TouchWiz/Stock crap calendar with something else on the market.
File Manager: There are much better apps on the Play Store for that than the crap that TouchWiz provides.
Backup: There are much better apps on the Play Store than the crap that TouchWiz and Sense provides. Titanium Backup and Helium?...You've never heard of those?
Google Music: I prefer Apollo(my favorite), and PowerAmp than the built in app that Sense or TouchWiz provides.
If the only reason you pick TouchWiz over stock is because Calendar, File Manager, Backup, and Music player are better than stock, then you must not venture out much into the Play Store. There are lots of apps on the Play Store that are much better than the built-in examples you've cited as what Samsung and HTC provides over stock.