Align kitchen cabinets to wall, or align face frames?
You want the faces of the cabinets on the same plane, and the entire assembly as close to the wall as can be easily achieved. On average, the wall and the cabinet assembly should be roughly parallel. 

If you're dealing with two sets of cabinets at right angles, you'd still want the faces of each set on plane, respectively, but you may not be able to keep a 90 degree included angle. 

In this case, your biggest concern is the countertop. A pre-cut 45 degree miter affords you maybe half an inch at the most of scribe-fit depth. You need more than than, which means you'll need your countertop miter pre-cut at a custom angle. That's not a problem if the shop measures in place, but if you're buying tops from a big-box store you're in for a challenge. 

Another consideration is how the cabinets align with any relevant patterns in the floor. Diverging lines can make a high-quality installation look shoddy in a hurry.