The E would obviously win
I don't care how much extra effort they put into the Vengence, it's 100 years old, it's tech is 100 years old, yes its souped up and beefed up but that doesn't matter, The E is simply a far more advanced ship
If you observe the Vengeance on screen you can clearly see the damage it can inflict on a fully shielded federation ship with just a handful of phaser pulses. This is a feat that no other 24th century era ship has accomplished with exception to the Borg cube firing at an Excelsior class ship at Wolf 359.
100 Years between 23rd and 24th centuries in regards to starship combat ability may mean very little if you just evolve the same old technology.
The Enterprise E has demonstrated on screen that it relies on phaser beams and unthreatening evadable photon torpedoes that need to fired in high quantities to do any real damage, just like most starfleet vessels did 100 years back.