Well, what effects and so on are you using? If there is a lot of footage and/or you use temporal effects, the frame lookup and footage I/O alone could contribute more to render times than actually processing pixels and that won't change no matter the final resolution. Also some effects will operate on the original footage size, no matter what since they bypass/ ignore the comp res downsampling. OpenGL based effects like Magic Bullet Looks for instance will always use the full res. if you want to make them use smaler resolution, you would have to pre-compose and only then add the effect on top. Could be several things, but there's a good chance that what you see is perfectly reasonable and normal.
Is there a way to customize output so that i can do something like everything but 3/4th line?
half - every other line
third - every 3 lines
quarter - every 4 lines
but no every 3 lines and skip the 4th line.
That's correct. You can't specify the line to skip.