I have observed that my ktm duke 390's back wheel is difficult to rotate even while its in neutral. If i'm riding the bike, if i put it in neutral, the bike slows down pretty quick than it used to be. Chain is well lubed and it's not tight. Any help ?
It sounds as though the rear-end is too tight. There is a straight rod which runs through the back of the bike which holds the rear-end together. You can see it in the circled in this picture:
If this isn't torqued correctly, it will cause drag on the rear end. Sounds like your's is torqued too much.
Another area to look at is to see if the rear brakes are dragging at all. This, too, would cause the issue you're talking about.