For many years in the 1960s, the Thruway Authority was opposed to creating an exit from the Thruway specifically for Interstate 88 due to the high cost of staffing toll booths. Ultimately they agreed but originally they had planned a connector at Exit 25. This was discarded in part due to concerns with run off from road salt into the Watervliet Reservoir.
You might call this image, why does US 20 flood so often in front of Stuyvesant Plaza. Filling in wetlands and creating vast impervious surfaces in the naturally pourous Pine Bush probably causes such things.