Technology has likely played a big part in the way the banks were merged. A clear pointer is the case of at least four banks; Canara and Syndicate and Indian Bank and Allahabad.
While Indian and Allahabad banks used BaNCS, Canara and Syndicate Bank were on the iFlex core banking system. Same technology means faster, smoother integration and massive synergies. This may have been a factor that prompted the finance ministry to go for these alliances.
The other six entities that were on the Finnacle CBS platform. The government opted to merge three entities each, probably as managing a single entity with 6 banks would be difficult.