To be honest, althouigh EWR is, as has been pointed out fairly congested, the bigger part of the problem is the relative lack of empty transatlantic seats, coupled with most of the eastbound flights coming across overnight. The lack of spare capacity across the pond means that when there is a problem, it's very difficult to arrange onward travel, short of adding an extra flight, which would be prohibitively expensive for the airline concerned.
The fact that the majority of eastbound flights are overnight flights is down largely to the historic attitude of BAA and the government that there should only be one gateway into the UK [i.e. Heathrow] and that the rest of the country should transfer at Heathrow. Fine in principle if you have a good network service at reasonable cost. However, due to the fact that Heathrow has a morning and night curfew, it can't operate 24 hours a day, so inbound flights have to arrive in a particular time slot. Now we have a much poorer network in the UK the model is falling apart.
Unfortunately, even although other services to other airports have been established, the way that the global timetables that have evolved over many years around the historic gateway airports are too established to let these other services really prosper in the way that they should.
As a fairly regular commuter through EWR enroute from EDI to IAH [should have been on this route on monday, but plans changed], I can sympathise with your problem and I've been very close to being in the same position on more thaone occasion, but so far have managed to squeak onto my connections. Generally I've found both Continental employees & airport staff to be pretty helpful when it's been tight to make it between flights. I can only sympathise with what happened to you, but at the same time I'd also say that a lot of restrictions are & have to be, put in place for safety due to weather forecasts, but the weather doesn't always live up to what the Met guys expect it to do.
Just accept that sometimes plans go adrift because of things we have no control over. As long as no-one is hurt, then that's about all we can hope for.