If I could do it all again, I would…

Without a doubt, first and foremost make sure to have an oversized salt water chlorine generator AND a large variable speed pump. A close second - an oversized cartridge filter.
Care and feeding of the various filter options can be discussed, and others considered. But the SWCG and VS pump is mandatory. Otherwise you are buying a very expensive puppy that demands the most expensive dog food, cleanup, and attention every single day. Every day. For years. No breaks, except for getting someone else to (usually poorly) take over the duty. The SWCG and pump resolves that, and makes owning a pool actually enjoyable.
Cut costs elsewhere if you must. Find another builder if they try to talk you out of it.

2 skimmers and floor returns!

my pool is 3.5' in the shallow end, do it over, a minimum of 4' in order to swim laps and not drag your knuckles.

Details matter. Even the small stuff that no one sees. I have looked back at my build photos over the years and thought, “man, if I could just redo …. again”. Pay attention to the plumbing layout. Make everything as accessible as possible without burying stuff under hardscape or placed in impossible to reach spots. Stuff breaks and fails and you need to be able to fix it without having to call in an excavator every time. Make sure your equipment pad (again, something no guests will ever see or care about) is accessible and easy to work on as well as protected from the elements. Don’t underestimate the need for automation … doesn’t have to be complicated and fancy but as long as you can rely on it to turn things on and off as-scheduled/as-needed, then you make everyone else’s time living with this pool easier. If the pool requires you to be there with some super secret notebook of switches and valves to turn, then you’re doing it wrong. Any idiot should be able to walk up to your pool equipment and know exactly how to use it first-try.

Don't put in floor drains. They are no longer needed with modern pools. You risk plumbing failures under the pool, tripping up your automatic cleaner, stubbing toes and they are just plain ugly.

Plan for extra electrical conduit around the pool and yard, so you can later run wires (more outlets, landscape lighting, ethernet, speaker wire, etc). You don't have to run the wires, just two or three runs of empty conduit you can later pull wires through. Once the deck goes down, this option will not be available. You need more than one, because you can't run both low and high voltage in the same conduit.

Run a few drip lines around the back of the pool before the deck goes in.

Same for water. You'll appreciate having a hose bib or two behind the pool.

Home-run each skimmer and every return with its own dedicated pipes back to the pad. Don't let them connect all your returns underground to one line, same for skimmers.

Home-run each light back to the pad, too. You can connect them together there, if you want to, or have each on it's own switch, to give you more lighting options.

Try to avoid pointing lights directly at the house or at areas you will most likely spend your time at night. You don't want the lights shining in your eyes or windows. This is another reason to have lights on their own circuits, because if you have to have a light pointing at you, you could turn that one off and turn the away-facing lights on, when you just want some ambient pool lighting.

Even if you plan on using a robot, run a dedicated vacuum pipe to the pool. It can be ignored, or later used for either a suction or pressure vac, in case you later decide to use one. It can also be used for manual vacuuming, or even another return in case you lose one. That line should be at least 1.5" PVC, with sweep elbows (so crud won't get stuck in tight elbows.

Be prepared for push back from the builder over some or all of the above. They like to build what they know, and not deviate. But it's your pool and make sure you get what you want, not what THEY want.

Here is my next pool list:

• 2nd skimmer
• I would research lights better and not sure I would have gone with my fancy color changing LED lights since 3 of the 4 had to be replaced under warranty. At $500+ a pop, I'm almost scared to use them now.
• That landscaping I didn't do during the build because I was tired of spending $ and could do it myself, still has not been done 4 years later.

Set the skimmers (note that it's plural) to benefit from the prevailing winds so that debris actually gets to the skimmers. Make plans for shade. I wish I had accommodated a shade sail. Give yourself plenty of room around the equipment pad so you can work on the various parts. Put in an auto fill for sure, with soft water to it if possible or if needed in your area. +10 on the SWG chlorine generator. And get yourself a TFPro testing kit before the pool is finished because the kit the builder will give you is wimpy and you do not want to be visiting any pool stores to get sucked into their business plan.

A shelter to help protect the equipment is nice, but it doesn't have to be a full on enclosed building. Mine lives out in the sun, snow, and -30F weather and has for decades. Others in hot climes really need the sun protection. If you get that salt generator, then your chemical storage needs will be little - a couple gallons of muriatic acid. Maybe a couple of gallons of liquid chlorine, just in case. Anything else will likely be drips and drabs of leftovers from once a year or so additions.

Shelter/shade/gazebos etc. for you, that can flex with the changing direction of the sun are a huge plus.

A nearby hose for the dogs, if needed before they go in the pool.

A heater is optional, but on Long Island, leave room for it, in case in the future it is not decided to be optional. Bring gas and electric for a future one to the pad. Will be cheaper now that to bring it in later. They do extend the useful season, but you can hear the gas meter going supersonic as it goes though fuel. (While electric is a viable option, you'll have to judge depending on your local rates. But it takes a LOT of energy to heat water...).

We normally completely distrust pool stores - but have a couple (different ones, so maybe the tests will be close to what they really are) should test your tap water. Calcium Hardness is the big concern. You may then need to plan for having an extension of your water softener to act as an autofill to counter evaporation. If Calcium gets too high, the only way to combat it is to replace most of the water. And that may mean trucking it in if your local water has high levels (a home softener just doesn't have the capacity to fill an entire pool).