While planning my upgrade, I had to ask many of the same questions. I went with:
GTN 650xi GPS WAAS navigator plus NAV/COM
GNX 375 GPS WAAS navigator plus transponder
10" G3x Touch PFD w / EIS
10" G3x Touch PFD/MFD
GFC 500 Autopilot
G5 backup
GMA 345 audio panel
Garmin remote comm - not sure of the number
The only non-redundant hardware is radio based navigation. I wanted both the 10" screens of the G3x which reduced the real estate options for radios. I went with the 650xi and the GNX375. The 650 is primary and the flight plans automatically cross-fill to the GNX375. If the 650 fails the 375 will take over GPS navigation. So I have dual everything except radio navigation. My reasoning was that with VOR's being removed from service, the redundancy in radio navigation wasn't worth the expense. Technically I have 3 GPS navigators but the G3x isn't certified for IFR use. As far as compatibility with other brands of equipment; it was a non-issue as I went with all Garmin. I previously had a G500 and it was a good piece of hardware, I find the G3x to be just as good and it is engineered to integrate with the GFC500 autopilot.
I am not suggesting that other options and possibilities aren't as good, but I couldn't be happier with my setup. Get what YOU want, since you are the one who has to be happy with it....and pay for it.
As a side note on radio based navigation - on the way home from MooneyMax yesterday, I heard two requests for VOR practice approaches and the controller told them the only way they could fly them is if they had a GPS that would shoot the approach using the VOR overlay......because the VOR's were no longer active.