Kyle Lowry is a binky of mine.
That said, as far as defense goes, I think they're peers at worst, favoring Lowry. But, I think that can be reversed, depending on preference. They are not, however, in separate classes. Defensively Rondo to Lowry is not a significant change, no matter which defender you favor.
Lowry is a better shooter, he scores with the same efficiency around the rim, and he gets to the line more often (which is counter-intuitive because Rondo goes to the cup more often, because he can't shoot).
Rondo is head and shoulders above Lowry in passing.
Lowry and Rondo are close in terms of rebounding ability, favoring Rondo.
Overall, Rondo to Lowry, assuming there is some regression to the mean for Lowry from where he played at the end of last season, is a step down, not a giant step down, but you're talking about going from a top 5 PG to a top 10. Its a difference.