Hey, you're getting ready for fun in the pool!! Do you have a design picture or diagram you can post? Pictures help so much like the great one you posted in September.
I'm not an expert, so hopefully more will chime in on your quote. I agree with Splash about the returns. My pool is similar in size, and I have 6 returns. My pool shape is curvy, so I'm glad I have each one. One at the top of my steps would have been great. Seeing the shape of your pool will help.
Your upgrades - here's some food for thought which may not work for you: Btw, I also have Jandy equipment. Are the 4 color LED lights all in your pool area? I have 2 in the main pool area and the colors work beautifully. Light coverage is great. A small light would have been nice on our sun shelf, but we're ok without it. I have the same Jandy heater - so far, so good. The experts on here really like the Raypak heater. Check the price differences and if a change from Jandy would affect your warranty for the other equipment. I have the CL580 filter (TFP encouraged me to go up on that). Since it's larger, I clean the cartridges only twice a year (unless we get flooding and my pool ends up a muddy pond!!!). My PB talked me out of the deck jets. He said they often clog, and any kind of breeze or wind messes with the pretty arc. I don't know how your breezes are. Is Crystal Lake in Illinois? Just curious - that still won't tell me how breezy it is up there! We're fine without the deck jets, but we don't have little ones around. If you have kids, that might be a different story. Check reviews on your Polaris robot - I don't know anything about that make. It looks good on your pump, but I hope someone else will confirm that. I have a 2-speed pump which works for us, but so many love the VS pumps. I love having the salt cell system. Using the TFP's steps in water management has kept that salt cell clean as a whistle.
A couple more thoughts - it depends on the average height or projected avg height of your family, but a 4 foot shallow end is becoming more and more popular. I just read a member (around 5'2", I think) say she wouldn't like the shallow areas to be less than 4'. And she has quite a few grandkids of all sizes. I've also heard others say a 6 foot depth isn't much of an advantage for jumping and certainly no diving. I have a 7 foot deep end which still means no diving, but jumping works fine. I also wanted a little deeper than 6' for exercising in the pool - don't want to scrape my toes. I like 7 feet for swimming down and just playing around. Let us know how you see your pool being used.
Post diagrams and renderings if you have them. The people here can give suggestions for placements of lights, skimmers, benches, steps, etc.
Take care,
Suz