Although most integration approach is to Assimilate, not just the operations, but the systems, there are instances in which the newco or even a brand new system is used for the merged companies. There are so many factors to consider that may lead to pitfalls, but here are a few:
– focusing at the financial analysis as the primary drivers.. instead of the operational impacts.
– trying to fit a round ball into a square peg… the newco business model is ignored (or not well understood) and focused fit into the parent co. ERP without much configuration
– resources not available… the right ones and not enough