CO has unlimited free upgrades for elites, but if you're a silver flying out of EWR those upgrades will likely be few and far between.

UA has free upgrades for (essentially) 20% of your flights. You probably won't get a better percentage on CO... and of course you can buy upgrades (with $$$ for certs, and always w/ miles) on UA as well.

Since UA isn't as dominant in NY, you'll likely do better.

As a 1P with UA (if you concentrate on one airline and get up to 50k miles or 60 segments/yr) you should do pretty well with upgrades.

Economy-plus is a BIG difference (especially when they block that middle seat next to you...) from regular Y. If you're going to be sitting in back at all, UA is MUCH nicer.

Their award availability is better. Their international route network (plus Star Alliance) is a real plus for earning miles/segs if you travel internationally or if you want to redeem miles internationally.

If you want non-stops, CO out of EWR is key. Of course, connections of UA to smaller destinations help you build miles and segments....