How exciting!
Floors: I have been in my "Dream Home" for 18 months by now. It has engineered hardwood flooring everywhere but the bathrooms. It looks fabulous and seems to be holding up well so far. It extends throughout the kitchen too, which is something I would not have done personally. However, much to my amazement that hasn't been a problem. I don't do a lot of extensive cooking although I do cook in there each day. So far, I was surprised that I have hardly ever spilled any water or food on it; maybe twice in 18 months. When that happened, I just wiped it up immediately and it did not damage the floor.
Popcorn ceilings: Under the circumstances, I'd suggest making that decision based on what will make your stay in that home happiest. It sounds like a lot of work to change the ceilings, and if they don't bother you then I wouldn't choose to change them. If, years down the road, you decide to sell, and if, at that time, your realtor urges you to do something about the ceilings, you can always deal with it then. Who knows what ceilings will be popular by then? I sure don't.
Countertops: My dream house has some sort of man made stuff that reminds me of Formica. Maybe that is what it is. My first instinct was to have granite put in, since I loved the granite at my old house. But, I decided to wait until the present countertops get stained, cuts in them, and/or become shabby looking (they look brand new right now). I have been amazed to find that these countertops, whatever they are, are so much better than similar ones fifty years ago. Maybe the advent of granite made these manufacturers "up their game", so to speak. So far after 18 months, being as messy as possible when I cook and not being especially careful, even (subconsciously) trying to stain them, it turns out that I have zero stains and zero cuts in my countertops. So, I'm keeping them. If/when they look bad, I'll do something but I doubt they will.
Shower: Ask your realtor about what sells or doesn't in your area. I suspect that having one tub in the other bathroom is enough. For me, the change you suggest (to a big shower instead of a tub in the master bathroom) would add a lot to the value.
Echos: Don't know if I can help you there. I have a lot of fake Persian rugs on my engineered hardwood floors, and these plus my furnishings cut back on echos.
Congratulations on your big move!