The thing with Star Wars / Star Trek is that either you consider they have the exactly the technology that is presented on the show (e.g. turbolasers are actually lasers), or if they are translated somewho (a turbolaser is some sort of disruptor).
With the translation, the technologies would be more or less matched - I assume space fights would happen like they do in the movies/series. The transporter would give Trek an advantage for boarding and ground invasion (I'm assuming here that the Wars shields work like the Trek shields), while the hyperdrive would allow the Wars ship to move faster (it looks like some kind of transwarp).
Without the translation... Trek would probably own Wars. Lasers have been shown not to do much to Federation shields and I'm not sure if the Wars shields could stop transporter beams or a photon torpedon. The hyperdrive and the Force would remain their biggest assets, but I don't think any Wars ship short of the Death Star could cause a significant threat to the Enterprise-E. And let's not get started on the Romulans / Klingons and their cloaking devices (although I guess the Force could help to sense them).
"The main difference between Trekkies and Manchester United fans is that Trekkies never trashed a train carriage. So why are the Trekkies the social outcasts?"
Terry Pratchett