The leaks and cracks I see aren't necessarily a problem, but they may be.

I would ask for a 2 year written warranty against leaks from those locations, specifying that more than 1/4" total loss in 24 hours, verified by the bucket test PLUS dye check of those locations indicating an active leak be sufficient to activate the warranty.

I would also try to take some better pictures of those cracks, using a camera capable of accurate focusing. You may need to put a pencil, or even a card with lines and text like "Crack #1" just next to the crack, so the camera has something to focus on.

The 1.5" variation between skimmer levels (how can you tell -- did you use a water level?) is enough to make me uncomfortable, and to suggest some sloppy work. It's not a show stopper -- most skimmers can handle 4" variation -- but it's enough to cause one skimmer to suck air when the other is fine. If you are correct about the difference, it would be more than enough to make me (if I was the owner) move in to what I used to call "toothbrush and flashlight" mode. That 'mode' is what happens when a pool owner's suspicion threshold gets crossed, and they begin to inspect everything with a "toothbrush and flashlight. It's a total PITA for the builder when this happens, because no pool is ever perfect. But if there is a genuine 1.5" variation, that's more than enough to make it a reasonable response on your part.