BINGO!!!I think is the problem.i reckon the power output of phasers and shields was a lot bigger on both e-e and defiant than on voyager, and they stored a lot more torpedoes. where all that energy came from on the small defiant is difficult to understand, it's power core looked a bit undersized, but it was a dedicated warship, and voyager is not.
I think we assume that sometimes bigger means more powerful and that because Defiant=warship, that any other Starfleet ship is weaker in comparision.
Indeed.
I actually proposed that the Intrepid is in fact a downsized Galaxy class.
Equal in shield/weapons output but overall smaller torpedo count and size while being faster.
The Defiant can probably rival larger ships because it doesn't have any luxuries on-board and most of it's systems were specifically made to fight the Borg.
The Intrepid is able to rival it's larger 'brothers' because it has a medium between luxuries and tech for combat.
The luxuries were downsized to the amount where it would be able to cater to a crew of only 150 leaving the rest for more powerful energy source, shields and weapons.
The Galaxy class is FILLED with luxuries in contrast and has to accommodate a much larger crew.
Bigger doesn't always mean 'more powerful' in Trek.

The Intrepid is nothing but bridge & cargo bays and very little of anything else.
The energy output in a larger ships goes to all other labs & operations that ship has.
The Intrepids have none of that to worry about and as you said, the power output is then put into sheilds & weapons. We saw it when it took at least 3 Kazon battle cruisers to try and bring it's sheilds down.
We've seen Voyager still go up against a Tactical Cube and it's shields held.
We've seen a Galaxy class go up against a Romulan Warbird and within to hits it's sheilds are almost gone.