I think Best Wishes was the better saga for a couple of reasons.
* There were rivals before the league throughout the saga. Rivals in general make for really solid arcs and episodes, though with flaws and needed improvements in Best Wishes. Even with these flaws, having rivals made for some entertaining tournaments and episodes.
* There being tournaments. The tournaments I felt were the best arcs of the saga, and unfortunately the Johto saga didn't have them.
* The non-plot related episodes were slightly more entertaining.
Aside from that, I see other things as making neither saga better or worse than the other.