Kawasaki has been selling both bikes in various markets - just because they share the same engine doesn't mean they're the same, and, having ridden both bikes I have to say that the engine feels pretty much completely different thanks to a different setup. If you let me blind-test both bikes I'd never get the idea that that's the same engine! It's _that_ different.
The ER-6n is basically a Ninja 650 without the farings - a naked bike.
So:
- Versys has more torque in lower revs
- ER-6n has more horse power
- ER-6n goes faster
- ER-6n is lower, Versys is higher
- Versys is more nimble (contrary to what you'd think)
- Versys is more expensive
- ER-6n looks better. It's stunning IMO.
There are many trade-offs - let's put it this way: The Versys is worse when it comes to horse power, looks, price, seat height - all reasons to want to buy the Er-6n

it's better for another variety of reasons of course but - different bikes.