Such as... ? Which particular ones cause the most concern for you?
First of all, you can individually select what goes to icloud. Look at Settings->iCloud (in the online manual if you must) to see all the on/off switches for photos, mail, contacts, calendars, etc.
From the trouble you mentioned, sounds like you and your wife are sharing an AppleID for iTunes purchases. That can definitely also cause issues if you share the same iCloud account yet want to keep separate data.
See the Apple Support documentation on using one APpleID for iCloud and a different one for Store purchases:
http://support.apple.com/en-us/HT4895
Agreed; however there is some variability in terms of the POS and whether it's set up well plus some process inefficiency until the ApplePay user builds enough familiarity.
Plus all the "easier to swipe" goes away with the ability to swipe at most places in a few months.