The general rule of thumb for EWR is that when flight operations shift from VFR to IFR there will be delays.
EWR's operational tempo is such that the airfield is completely maxed out in terms of # of operations / hour under VFR conditions. IFR brings with it a regulatory requirement for increased separation between aircraft on take-off and landing. This reduces the effective number of operations per hour and delays are a mathematical inevitability.
Note that major airlines will cancel fights under these circumstance. The canceled flights are not, themselves, specifically due to weather but are instead due to the aircraft schedule juggling that has to be performed when there are multi-hour delays across the board..
Example: You're scheduled to fly out of EWR to Tampa at 1PM. Your aircraft is scheduled to fly inbound to EWR from Charlotte. It's scheduled to fly out of Tampa following your arrival, headed for Houston. When the delays pile up United will cancel the CLT to EWR and EWR to TPA legs and send the aircraft directly from CLT to TPA. The result is 2 flight cancellations, but they avoid the cascading (i.e. increasing) delays throughout the day, which can impact gate assignments, connecting flights, etc. Lesser of 2 evils.
