I have an aimpointml2 with standard ar15 fixed front sight. It is set at 100yrs with dot on top of sight. Would it be better to replace the fixed sight with a pop up and use the red dot only.

It is really up to you on if it bothers you. I have an eotech on one, and an aimpoint on another and both have fixed front sights. Dont even notice them. I personally don't like folding front sights, just prefer to be able to bring the rifle up, and if the red dot somehow went out, flip up the rear. Figure its just an added step to have to reach up and flip up the front too. But I am lazy...

I was wondering how accurate it would be without the front sights in the picure

Oh. Thats not how they work. You dont need to put the dot on the front sight and then on the target. Just the dot on the target. You dont even really need anything other than the dot except as backup.

changing that A2 front sight is a MF compared to a different upper I would go with a co witness if you do not want to change that bareel if you choose to go w a 1- 4.5.6 - 20x in the future that sight will blur the lower magnification...choosing a red dot seems to go with <100 yard shooting and front/rear sighs are consider BU.. so my answer would be use only one device to aim hence that Aimpoint red dot

Thanks for the input.