#1 - I actually like the sound of the motor when you mash the accelerator. Not noticeable most of the time to me.
#2 - I don't notice the muffler. Go to a dealer and look at one...If you can find one. There are also loads of pics on-line at the Toyota web site.
#3 - Like almost all cars today, there's no way to shut off the Start/Stop permanently. Just push the button each time you start the motor. I've gotten into the habit of it when I reach for the shifter. It's very easy to access. You can thank your EPA for that one. I had a '17 Jeep Cherokee, and the V6 motor shook the car violently when re-starting after being at a stop light. I got in the habit with that car because it was SO annoying! The Cross is much less so. Sometimes you can hardly feel it. I shut it off because I don't like the wear and tear on the engine/starter/transmission. There might be something aftermarket on the internet that shuts it off automatically at each start-up. Designing something with a simple 555 timer that closes that button connection a few seconds after start-up would be really simple.
#4 - My only complaints are related to #3, and that I'd like to have a bit more power on-tap when needed...But that would likely compromise the excellent gas milage (I get 31-33), and might cut the life expectancy of the drive-train. So, I'm, ok with it as-is. A tubo could give it 100 more HP, but would likely cut the life in half. I'd rather have it last 300k miles, even though I might need to wait a bit before I pass someone on a 2-lane highway.
This is my first Toyota. Overall, at about 1600 miles later, I'm very happy with my purchase. Originally I was shopping for a Rav4, but couldn't wait the 6 months for one that wasn't already spoken-for. The dealer had a XLE AWD coming in 3 days that was un-claimed...so I took it...even though I had never heard of a Cross before he showed one to me on-line.