iMessages,Facetime notification sync issue

Right...

Excuse me if this is a daft question but I need to get this sorted as it's driving me mad!

I have an iPhone 6+, iPad Air both running the latest iOS 9 and a 2011 iMac running El Capitan. The issue I am about to describe has been an issue for since iOS 8 and using Mavericks.

I use all three devices on a regular basis and I have always enjoyed the way they function together, all except for this issue....

If I receive a message on my iPhone and aI read it and delete I would have expected it not to show up on either my iMac or iPad but this is not the case. I have to go into messages on my iPhone, iPad and iMac to delete it. Deleting the message from one device does not delete it from all three! is this just me or does this defeat the object of the whole joint functionality?

Equally just as frustrating is FaceTime, and has actually got worse since El Captian. Obviously like most people I use my iPhone a lot during the day for calls etc... but when I get home and check my iMac it has the little red circle in the corner of the FaceTime icon with a number. This number represents the amount of incoming call i had received throughout the day. So in short for every incoming call I receive, wether I answer the call or miss it, I end up with the red notification on my iMac. Surely this should vanish once I acknowledge I have missed a call on my iPhone? The second issue I have is that if I answer a FaceTime call on my iPhone or iPad then my iMac will again show up a red notification over the FaceTime icon as if I had missed the call despite me having answered it on another device!

I accept this is trivial but it is frustrating having to go through my messages on each device and clear them out. One device should sort all the devices out surely?

On a bit of a side note... I have also noticed that if I get an incoming phone call or FaceTime call on my iPhone when I am home on my wi fi network then there is a significant delay in my iMac and iPad ringing swell.. sometimes long after I have answered the call. Any ideas on this and could it all be connected?

Good luck with this one... hope someone out the