I fully intend on going with all of the water and light features.
Sounds like you went through the mental process and have made peace with your decision, that's excellent to hear! If you can do it now, and want to do it now, and are confident in the decision, that's great news!
Each group of lights you want to individually controlled needs to be wired to its own light transformer and each light transformer will require a relay in the IntelliCenter.
With all the planned lights, and you want to control them in groups, the only way to do this is with multiple transformers. Depending on how many groups you want, that would be the number of transformers you need.
I will have to find out how they plan to place the skimmers and returns and then try to fill in around there
Do a little research on the "prevailing winds" in your area. Not all builders think about the ideal placement of skimmers, but if you get them in the place where the prevailing winds will blow the debris to, you will have a much better result out of your skimmers. Wind can be a big factor in blowing your debris around the pool, and if your skimmers are out of place, the stuff can just float around and never make it in.
Once you have that set, you can figure out the placement of the lights. It will be an interesting look, because normally you want the lights facing away from the house. Your pool will have the short side away from the house and can probably only get one or two lights on that end. You will have to get creative on pointing the lights so they do not shine back into the house, or into your neighbors windows, but have seen a lot of creative light placement here, so it shouldn't be all that bad.