Critique my (possible) new system. Suggestions welcome!

Congratulations on going with an integrated and stereo. This is the sweet spot of dual-use. Amazing how far you can go with this. Well done.

If you have heard all this stuff and like the way it sounds that is all that matters. So no point critique there. 

What you need are Synergistic Research interconnects, speaker cables, and power cords. There's a ton out there used. The beauty of SR is their consistency of performance over many years means you can safely buy whatever you find regardless of whatever your budget may be. I've been using it since the 1990's and its all good. Better than good.

Components and wire only get you about half way there. Two-thirds at best. The rest of what separates the stellar from the average is details like ECT, HFT, fuses, Total Contact, and really good setup.

Not kidding, the details make all the difference. See my TC review posted today, search around for Total Contact, Synergistic HFT, etc. That's et cetera, not to be confused with ECT! Read mahgister. These are the things that make your system disappear and float mesmerizing images that will astound and amaze.

Why do you need the Yamaha  for HT bypass if you're only doing 2.1?

For video processing? I’m not sure I can connect everything through the Lyngdorf without the add on HDMI module which I do not have. I guess I’m not really sure to be honest. I figured it would be easier to keep the Yamaha and have all video components run through that, keep some flexibility for the future if I added a center channel or surrounds and let the new stuff handle the music listening. The AVR is only a year or so old but I’m still learning about all of this stuff. 
What would you suggest?

If it's  fairly  new and you might add more speakers then I would keep it and use whatever new integrated amp you have for the l and r front and let the Yamaha do the res. Makes sense if you plan on adding surround  you only mentioned 2.1 in your original  post. 

Ya I would nix the A/V receiver and run your video sources direct to the tv and their audio into the Lyngdorf. Keep it simple. Think about adding a second sub configured for stereo. The idea that deep bass is monaural is not true. Also introducing bass from a second location usually evens out the bass response in the room. Try to put one sub near each speaker. One other tip for better imaging is to cover the TV with a heavy blanket when listening to music. Having a highly reflective surface between the speakers can mess up their ability to create a 3 dimensional image of the performance.
You will be surprised how good an experience can be had with a two channel theater system. Much simpler and less expensive.