Ok, here go my thought in no particular order:
1, Dump the Nature 2 system, we strongly advise against them around here, (green hair, pool staining, etc.) if you want to know more details of why just search the forum on Nature 2, there will be hundreds of threads about them.
2, Home run all the returns, it does not cost much more, and if you ever get a underground plumbing leak you can isolate it and potentially put off fixing it until the off season rather than jackhammering up your pool deck in the middle of the summer and loosing use of your pool for weeks.
3, I also note it seems like you only have one skimmer listed, I will not say you must have 2 or more, but for most people it helps, but this depends on local wind patterns, where I live the wind tends to blow from the south in the summer and the northwest the rest of the year, you want skimmers placed on the downwind side of the pool, so that means around here most people need 2 one for the summer wind, one for the rest of the year.
4, Make the pool deeper if you are going to have a diving board and make sure the slope of the pool going to the shallow end if far enough away. There are detailed diving profiles listed on the SR Smith web page for each model of diving board they sell. Personally I feel a 20x40 ft pool is about the minimum size for a safe diving board pool. Even then there is a need for caution when diving head first so you don't kiss the slope on the way up.
5, Consider making the shallow end a bit deeper, just 3 or 4 inches makes a lot of difference here, also we often see gunite pools built shallower than specified as they often make the pool bottom thicker than planned when shooting the gunite so even if you spec a 3'6" pool you may end up with 3'4" or 3'3" (also make sure those specs are to the water line not to the edge)
6, I second the bit about a pool robot over all other pool cleaner options, as down the road when it needs to be replaced, it is MUCH easier.
7, Get more details, which exact model of pump and filter are they trying to sell you, which exact model of automation system, ...
8, Strongly consider an SWG for chlorination
That is all for now my wife is telling me I need to go
Ike
p.s. also that second light, and you need to remember Pool Builders may or may not be good at building pools, but most know NOTHING about living with a pool