The new leaves are much darker green than the older leaves which indicates a shortage of nitrogen.

Did you fertilize? If not, do so now. If so, probably needs more.

The ones with the dark green leaves (not pictured here) are doing much better than the light colored ones pictured here.. Maybe you meant that the other way around? On any given plant, all of the leaves tend towards about the same color for that plant.

Well, in the top two photos, I see a distinct difference in the top most leaves and the leaves somewhat lower down -- inthose 2 photos, the top leaves are darker green than the lower leaves on the same plant.

There will be some slight color differences on the plant itself, but it's not really uniform from what I've seen. Some will be lower or higher leaves - though a lot of the brand new leaves do tend to be darker. I don't consider the darkness to be a sign of problems though, I've always held it to be a sign of health. All of my really healthy plans are very dark compared to these. I pulled one of the troubled plants over next to one of the healthy ones for a picture so you can compare:
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Further shots of some of the healthy ones including the fruit:

(Hungarian Sweet)
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(Orange Toro Sweet Bell)
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The guy that's suffering in the first pictures is a Italian Sweet Bananna Pepper. The dark one in the picture with him is a Hungarian Sweet. Though I can't say for certain (would need to do better testing), the use of Epson salt seems to help bring out the deep green and promote flowering. Between my posts I've applied some to the plants in trouble to see if that might help and I'm starting to see some color change, though I still can't say that the plants look "good". I did use some nitrogen earlier this year - Calcium Nitrate because I didn't want the Nitrogen to lower my PH on me. Application was within guidelines thought I saw some signs that the plants may not have reacted well in some cases (had so many things going wrong at that point that nailing down a specific cause would be impossible). I do believe my primary problem from then though was simply the cold weather. Nothing I did had any real positive effect on my peppers until it warmed up. The temperature was hanging in the 50's for weeks on end and I think the plants just couldn't get the nuietrient uptake they needed at that temperature (there was a brief aphid problem as well, until I got that dealt with). I kept most of my plants inside under grow lights instead of putting them out until I felt comfortable with the environment outside again.