I'm with Analise, you're coming to Northern New England on Labor Day weekend, and so is the rest of the world (or so it will seem). I'm predicting you'll hit traffic snags in at least New York, Massachusetts, and Maine, possibly New Hampshire too. Obviously I hope I'm wrong.
I'm not sure there is much you can do to avoid traffic heading to Maine because of your timing, but going from Bath to Acadia on Day 2, I would take I-295/I-95 North to Bangor then head east from there, otherwise you'll hit traffic in at least Wiscasset, Thomaston/Rockland, Camden, and possibly Belfast and even Bar Harbor once you start to get near Acadia. Save driving up coastal Maine for a time when you have lots more time to kill, your itinerary doesn't seem to allow for that on this trip. If Acadia is, as you say, the main event, you'll never get there in a timely manner going up Route 1.
From newest to oldest, the hotels you listed would go in this order: Hyatt Place, Hampton, HGI, Doubletree; Hampton and DT are definitely nice, haven't stayed at the others. The DT is actually located in South Portland, right across the street from the Maine Mall. If you want something downtown, you'd want one of the other three.
Day 3 looks fine, but if the weather is crappy (which it's supposed to be), indoor things are likely to be a zoo, so keep that in mind as you look at what specifically to do in each place.