My chip out looked like what you're describing. I don't recall seeing them do anything after that. They just smoothed it all out with my pebble finish. As other's pointed out, an acid wash won't fix that, not even close. An acid wash removes material in the 1/16"-1/8" range, if that.
Now just about any pool finish is going to look wavy and bumpy, to some extent, and that is normal. Even the most carefully applied finish has those types of imperfections because the finish work is done by hand troweling. But you shouldn't really see that during the day. At night, the angle of the pool light makes the bumps look gigantic, and most people (including me) freak out the first time they see their brand new finish at night. But if you're seeing that during the day, that's a red flag.
Now I don't know what a Micro Fusion finish is, or why it is applied with multiple coats. If it's more like a spray-on coating, then Allen's right, the chipped out surface (gunite?) would need to be prepped smooth somehow, otherwise any imperfections would show through, the number of coats wouldn't matter. Does it come from a manufacturer that warrants the product or its installation? PebbleTec finishes come with a manufacturer warranty, and their installers must be certified to install it. Anything like that for Micro Fusion? The reason I ask is, if you are not satisfied, and your contractor won't do anything about that, then you might be able to get a rep from Micro Fusion to come to your pool and assess the installation. He may side with your contractor, or he may side with you, but at least it's another opinion you can gather to see if your expectations are realistic or not.
If you can capture what you're talking about with some pics, and post them here, our experts might be able to help you with that.
You're going to have to move fast, they're going to want to put water in the pool immediately after they finish acid washing. Of course, maybe it will look better once filled. Mine did.
