Sounds like a plan
I'd say you have it all covered fairly well
-There's nothing wrong with having Comcast as an ISP. In fact, they have rolled out DOCSIS3 service in most of their service areas. That would be the logical upgrade path, along with upgrading your SB5100. For about $80-100, you would get to access the channel pair bonding that really speeds up your cable broadband service. Look at Amazon or big box store prices on the Moto 6100 series. Nice stuff! Understandably, you might not want to fork over $65/mo for broadband service though.
-Running ethernet to your Denon is perfect. I do the same thing with my older Onkyo HT setup from an airport express. Works fine, even on my older receiver using mini-toslink to toslink. Great way to stream from iOS, etc. I also use VLC as a media player sometimes. Works on Mac too, I believe.
-There's really no way to create a 'standalone' DVR by adding a HDD via USB to your Denon. You could however employ some sort of software solution to record programming on your mac if you installed a TV tuner card, and used an external (or internal) drive that way. I am more familiar with that avenue in the PC world unfortunately. Same principles should apply though.
-RG6 cable is wonderful, along with your current connections/splits.
-Netflix app on the Panny is fine (I set my parents system up this way), but make sure you run ethernet from your repeater or router directly to the E3 HDTV. Much better in the long run than dealing with netflix over wifi IME.
-Yes, now there are many ways to stream various content, it's almost ridiculous, really. I am still partial to doing so on the desktop environment and sending it along via HDMI to a large HDTV. IME sometimes the app quality on the various blu ray players or HDTVs leaves something to be desired.
If you have more specific questions, feel free to ask