I own a manual 1.8, resale obv. would be less than top of the line variants, but trust me the pleasure of driving a manual, that too the new civic is something worth having, ive had the car with me for 2 years now mashAllah, and i just love the feeling it gives, the way you get to choose between the powerband you want according to your own perspective, thats all what matters, driving pleasure and a bit of fun.
Having said that i would also like to advise to you that if you travel in rushy areas a lot, then get the pros, otherwise if you have a driving route where traffic is moderate or sometimes more than that, then manual is the car for you since you're going to buy it brand new, and its your personal car; auto civic is also a joy, but trust me the manual puts a BIGG smile on your face, sometimes you're just in the zone to play with the gears.
As for the resale, this is Pakistan, im sure after 3-4 years people might get it off your hands for the price you paid for it, or even 20-30k on top of that, 2005 civic's are sold for much more than their price these days, so yeah anything is possible in Pakistan.
Fog lights, not an issue, you could get after markets
Sunroof, just a shashka for 2 3 months, uskay bad im sure you wouldnt even bother using it.