You make some good points but also you can't lay it all on Nathan Lyon as being the primary reason we didn't win some of those games.
That Ben Stokes innings for example, Marcus Harris drops one in the outfield, Nathan Lyon also had one of them dead in front but Tim Paine elected to waste a review on one that pitched outside leg (not sure exactly which batsmen was on strike, would've won us the game whoever it was). Sure he made a meal of the run out attempt but anyone can make those mistakes under pressure.
As for India, they grow up on spinning low bouncing pitches, if there was ever a team in world cricket you'd back to take down a spinner, it would be India and it absolutely would have been in their team talks, as it would be for any team. Take down the spinner and expose the quicks, that's how you break down any attack.
It would be nice for him to completely destroy a batting line up but the reality of it is that very few spinners are capable of that, not since Warne/Murali have we seen someone who can consistently do that. Ashwin on his day against the right line up on a pitch that suits can do it. I don't know what you expect him to do, he does a more than serviceable job and has extracted every ounce of ability that he has to be one of the most consistent bowlers going around and I think that's the keyword for Nathan Lyon, consistency. There is nobody else we have in our stocks that could do a better job, I know you grew up watching "the spin king" and that's probably what you expect of any bloke who steps into the team to bowl spin but it's not reality. He is probably the greatest we will ever see, Shane Warne that is.
I will give you the spoiler, the next bloke who steps in won't be as good as Nathan Lyon has been, let alone Shane Warne. So I look forward to you plastering that bloke, too.