The main advantage they have is FTL that doesn't do really damn funny shit to ships, like dissapearing them, screwing with time and generally speaking being dangerous to users. As for the firepower and durability I guess WH40k Imperium wins, most of the time. The under-ftl speed is also proably higher in the SW designs, but on the other hand they're also much smaller usually. Also, Imperium of The Man seems to have much bigger fleet, but it seems to be also more spread-out, mainly due to the FTL problem. If we could manage to get that FTL tech into Wh40k and convice Mechanicus that it's not FUCKING HERESY, we would pretty much win the never-ending war for the Imperium.
As for the ground - the lasguns are proably at the similar power as the common blaster (also, hotshots exist and stuff) but - as unbeliveable as it sounds - the WH40k flak armour seems to be better than most things they came up in Star Wars on mass scale, since they apparently can protect the user from stray lasgun shoots or even bolter rounds (!!!, I remember reading about that somewhere). The vehicles vary on quality but I would say that still, Wh40k usually wins and even if not - they have much more of them.
Then again, setting up a second empire is HERESY. There is only the imperium, and this one, even in it's current form, is no exception. We are a servant of the emperor, not his regent.
I don't see why those two things collide. After all, we will be serving the Emperor and Imperium because we're clearly the only person around who can do that, since, you know, we're the only ones who actually know who The Big E is.