It depends if you limit the higher level Sp/Su available of the higher CR DM Monsters under the same rule.
In E6, you're never really expected to deal with probably anything higher than CR12.
Otherwise you end up losing the war against things you're supposed to intelligently be able to counter or recover from.
For instance,
no Dimensional Anchor to deal with Teleporters/Plane Shift, common among higher CR outsiders
no Disintegrate to deal with Forcecage or Wall of Force
no Greater Dispel Magic to deal with ever increasing CLs
It can work, and it'll feel gritty, but the DM has to be careful not to present something that is uncounterable.