I would say this is a tough call. A lot of it depends on where you fly. If you do a lot of Europe, then CO has better Germany and UK, but DL has better Italy and France. And so forth. Overall, though, please note that CO is--by far and away--the airline with the most departures out of the NYC area. Also, while JFK may be OK for you (I prefer JFK to EWR because I live and work in Brooklyn), you are clearly well aware of the profound state of decrepitude of both of DL's terminals at JFK.
If you've been receiving upgrades regularly on DL, then I would say DL has the edge here. CO has changed its upgrade system over the years and now a free upgrade for a low- or mid-level tier elite has becoming increasinlgy difficult. Please note that this is especially the case for CO flights in and out of EWR.
I don't think there is any possible correlation between carriers and fares. On the other hand, though, CO deeply discounts its BusinessFirst fares (its international premium class, the equivalent of DL's BusinessElite) both in the winter and the summer. Given the high quality of the product, buying one of these discounted business-class fares on CO is one of the great airline bargains going (I've flown CO in business EWR-CDG for $1,200, EWR-GVA for $1,400 and EWR-TXL for $1,100) Please correct me if I'm mistaken but I have never seen any regular discounting of this depth of DL's TATL business class product. Elite is easier to maintain with CO, since its highest tier only requires 75k miles. But the real question is what good will it do you? If you're often unable to receive upgrades, and award tickets prove to be as hard to snag on *A as they were when CO was ST, then it's pretty much just a plastic card in your wallet to stroke your ego. The advantage does probably go to CO here, especially with their entry to *A