If it were mine, I'd first install whatever counter top the Boss likes that has a built-in (4" tall) back splash (for ease of cleaning), butted up to the high spots on the walls. Then I'd install the thinnest cementitious tile backer board I could find (1/4" or 3/8"?) on the wall between the top of the back splash and the bottoms of the upper cabinets, using inert shim stock under it in the wall's low spots and using appropriate screws to attach it firmly. Then install a pretty ceramic tile (I like 4" in kitchens) with some random, eye-catching "highlight" tiles, maybe complementing some of the pattern in the counter top. With a sealed and contrasting grout in the tile joints, it would look like a million bucks, last forever, and permanently hide the waves in the walls. And with the right combination of back splash, backer board thickness and tile/adhesive thickness, the finished tile surface could be made just flush with the back splash surface--meaning there's no "lip" to catch dirt and grime.
Sounds like a lot of work, but I've done several jobs as described, and it's not really that involved. And the owners were both tickled pink with the results. Think I could have charged each of them double what I actually did, and neither would have complained. One woman did grumble that she had to buy a new, shorter coffee-maker, as her old one didn't fit between the new synthetic granite counter top and the upper cabinets. Tisk, tisk.