Looking at their career stats they are not all that far apart in scoring, rebounds, and assists with lowry having the edge in each. Hill still the more efficient player. Lowry played in a role where he handles the ball a ton and has a ton of usage. Hill didn't. They played different roles.
No way to know how they would compare in similar roles. I have always probably over valued efficency though so that might be why i feel different than you on this one.
This season though in his new role with his new team not only is hill more efficient but he is also averaging more ppg when you adjust for the same amount of minutes.
It could be argued (though i think its not worth much discussion personally) that since hill has been in the league for 2 less season and played less minutes per game and less total games that hill has less mileage on his body.
Their career numbers might be closer but the last 4 years (which matters more than 10 years ago what they did) since Lowry has really taken off they are not close statistically. Lowry took awhile to get good.
As far as injuries go I only care about lately. Lowry missed almost his entire rookie year but obviously that is not a factor since it was 10 years ago. Maybe Hill has had bad luck 2 of the last 3 years or maybe his body is breaking down more? I dont know. 2014-15 season might be the best comparison for the two since they played similar roles that year, they are not that far off that year Lowry put up a lot more numbers in most categories but Hill was a little more efficient. I dont think the gap is big but I still take Lowry.
I put Lowry pretty high on my list right now. I put him behind Curry, Westbrook, Harden and probably CP3. I put him in the same tier as Wall, Lillard, Irving, Thomas and Walker.