Now I know both are completely different, but here is what I am looking for:

1.) Daily use within the city+highway (As I ride to work over the highway)
2.) 1 long ride in two months.
3.) Mileage is not really an issue, but should not be ridiculously low, like below 12.

Both bikes will deliver good mileage. GT should give around 15..

But be aware that this is a V-Twin. It will deliver good torque, but don't expect it to run below 3000 rpm without snatching.
Although again, Ninja has lesser low end torque that a common street 250. Run in period will be real slow & tiring!

Long ride should be no problem. Both are sport machines, so think about it before using them in city. Might need lots of gear shifting.

4.) Should be comfortable - I am used to a sporty riding style, but I have heard that the Hyosung gt 650R gives way too much vibrations. Also the pillion position in the gt 650 r is a little high, ( MY gf hates it :P) but it has a grab rail now. - In put on that ninja pillion riding position please.

GT vibrates above 6500-7000 rpm and sportier riding position. Ninja is smoother though. Ninja has more reasonable riding position. So, for comfort, Ninja might do the trick better.

5.) Practically usable in the city as well as the highway.

People have used Ninja 250 and one guy says in its 4krpm run in limit, that its low end torque is lesser. Prepared to do some gearshifting, but overall you can live with it.
Don't know about GT.

7.) External styling, Oh man I love the looks of the 650R.

Subjectively speaking, I agree GT looks better to me than N250.

Don't forget that the engine/ tyres are much bigger on GT.
Ninja on the other hand is good enough, but again, how fat a tyre can a 250 have?

8.) Reliability, the Ninja would gain higher points over this.

Only because, GT wasn't in our market so far. Who knows it might be reliable enough inside?

10). Service Backup:

Well, you can get Ninja serviced (now) in more places than GT. But again, GT are aiming for a Mobile Service option that could help you, at some serious expense though.

11.) Performance - Hyosung

Yes, GT for performance.

12.) Handling - no clue haven't ridden the 650

It has good handling if you trust reviews, its derived from some Suzuki's 650.

13.) PRICE tag - this is where the ninja takes the cup, but by compromising the performance to 1/3rd

Yes.

14.) Delivery period. The Hyosung guys aren't sure themselves. Ninja - people input please.
15.) Resale Value.

Talking percentiles of bike's cost, I think you'll get better value for N250.

Kawasaki's brand value matters, plus resale values are good for existing Ninja owners. I heard one was selling a N for some 2.1L.

16.) Bike's response - Throttle response and Braking.

Braking was critisized in a lot of places on GT. But, could have changed for 2010. Try getting more information on this.
Moreover, an EBC Brake pad would solve the issue if it still exists.