Future's End: Intrepid class vs Aeon class - Voyager is able to withstand several attacks from the 29th century ship end even overpowers it.
A small, one-person ship. Evidently Braxton just happened to survive the explosion in the future and took matters into his own hands, so he had to use the tiny shuttle he had rather than mustering a more effective battleship.
I was under the impression that energy weapons are more effective against shields and torpedoes against armor.
Well, as I mentioned above, real physics says that dense physical armor would actually increase
the danger to the crew from charged-particle weapons, because those weapons would cause the armor to emit lethal x-rays. And since most "energy" weapons in Trek are actually particle or plasma weapons, that means that physical armor should be literally worse than useless against beam weapons.