Well there are 2 issues.
1. Era vs. Era fighting - when ships from different centuries fight each other
In a Mirror, Darkly: Constitution class vs Vulcan cruiser - easy win for the Defiant
Future's End: Intrepid class vs Aeon class - Voyager is able to withstand several attacks from the 29th century ship end even overpowers it.
2. bonus vs.
I was under the impression that energy weapons are more effective against shields and torpedoes against armor. But that doesn't have to be always true and on the other hand the the ablative generators could be less impregnable to Borg weapons then Klingon weaponry.
A possibility is that they did not installed the generators at full efficiency. Janeway was not an engineer and she perhaps only brought the technology and not exact blueprints.