I've never really understood why people say this. The atmospheric system worked (when it worked at all) by pumping the air out of the pipe ahead of the train, so its tractive effort was theoretically limited to one atmosphere multiplied by the cross-section of the pipe. In practice it would have been considerably less due to imperfect vacuum and friction.
Thank goodness someone else has noticed this, I thought I was the only one. That the atmospheric system "makes light of gradients" is true only in that wheelslip no longer comes into it. But limitations on tractive effort from locomotives can be resolved by using bigger or more locomotives, essentially without limit. The atmospheric system, on the other hand, imposes a hard limit on tractive effort which in turn means that there is a certain maximum weight of train that it can haul up a given gradient. They were lucky that the bit they did install proved troublesome enough to put them off, because if they had installed it over the banks, 22-inch pipe notwithstanding, they would still have had to rip it all out again or else be forever limited to 1840s train weights.
Also, the gradients were not the consequence of the route being selected with atmospheric traction in mind; the atmospheric suggestion came in a few months
after the route had been decided. It wasn't a case of "we can ignore gradients because our technology will make them irrelevant", it was "we're stuck with these gradients, but maybe this technology will make them less of a problem than we thought they would be".
It is not possible to get from Exeter to Plymouth without heavy gradients by any route; I suspect Brunel's aim in choosing the route he did was to make as much of it as possible trouble-free, and concentrate the difficulties in one circumscribed area, so that the special measures needed to deal with them did not affect the ease of operation over most of the route. Much like the London-Bristol route where he concentrated the gradient into the Box stretch and left the rest of it nearly flat.