All Hondas are inherently uncomfortable. My 2002 VTi is very uncomfortable as well. And so was my 1989 Civic---this car was UNACCEPTABLY uncomfortable---suspension was on par with the Suzuki Swift of that time.
While driving one of my friends 2006 City, I thought the City was slightly more comfortable than the 2002 Civic. Strange but it at least feels that way.
Sorry bro but you have to live with the hard and rough suspension. Thats what you get for a higher ground clearance car. Pakistani models have a modified suspension to take care of the road conditions and the uncomfortable thing is just a side effect of the suspension tuning.