I use Google Maps for general map usage but Garmin for actual navigation, Readdle Calendar5 (on the built-in calendar's database syncing via GMail), my contacts sync via GMail, Safari bookmarks sync via iCloud to my desktop Firefox with Apple's Firefox add-on (and is the main reason I don't use Palemoon instead of FF - this add-on does not work in PM).
Music/video/photos are synced via iTunes on my desktop not OTA through any service except podcasts, which are downloaded from iTunes online directly to my iPhone via Apple's Podcast app. I have eBooks in both iBooks and Nook software. With maybe one exception, the difference in management there for me is free vs purchased. I like my media to be cross-platform, so I refuse to buy eBooks from the iBook store, but iBooks has better rendering of the ePub format and better e-bookshelf management.
I use Microsoft Office and despite Apple claims otherwise, iWorks is NOT truly compatible so I use MS Word and Excel on my iOS devices, accessing OneDrive for most of the files I need, Dropbox was just added, I keep some there for other activities. Not really covered by your question, but I use Readdle PDF Expert for PDF files
The only real sticky bit in my setup is maps. IMO, Apple Maps still sucks. Last time I checked, it still has multiple addresses and businesses that I know of misplaced by as much as a mile, sometimes on the wrong side of a divided roadway. But there is no way to tap an address in, say, Contacts or from Safari and open it in anything other than Apple Maps. One of the reasons I use Calendar5 is that it has a setting to open appointment addresses in Google Maps instead of Apple Maps (CalenGoo has that same feature). So for most applications, if I want to map the address I have to copy it and manually open GMaps or Garmin and paste the address into the search. I do it because Apple Maps simply sucks.