One of the nice things about the Greg Bear story I mentioned (and its sequel, "Anvil of Stars", that I actually prefer), is that the aliens don't have faster-than-light drives. So far as we know, those are impossible. Instead the aliens just spent a long, long time travelling. Relativistic affects mean the time is shorter for them, and we shouldn't assume they have human psychology, physiology or lifetimes. For example, they might be machines that can shut themselves down for the journey.

(I agree about the EMP, though. If they can get here, they are probably massively superior to us. Niven et al's "Footfall" is a novel where this isn't true. Fun but unlikely.)

I figure the two most likely scenarios are religious advocacy, or pre-emptive strike.

Within human society at any rate, first-contacts have historically often be done by religious missionaries who want to convert the heathen natives to whatever god or philosophy the missionaries favour. If aliens want to convert us, hopefully they don't want to kill us. Of course, they might also be motivated by a form of racial (or inter-species) hatred and see us as vermin and an offence to their god. With religion, almost any belief system is possible. I wouldn't assume that a species capable of space travel would be rational in other ways.

In Forge of God, the motive is self-defence. In the book it's possible to build robots that can travel to a star system, take apart any inhabited planets and use the parts to build more robots. Rinse and repeat, forever. Given that other species can do this, each civilisation ought to build their own killer robot fleet to wipe out everyone else first. It's a race.