Firstly, clubs often had difficulty agreeing dates, and the tournament struggled to finish on time - for example, the 1964–65 final wasn't played until early June, over a year after the group games had started; and in 1963–64 and 1965–66 it was concluded in late May.
This meant that clubs who had progressed from the Intertoto Group Stage, but were also competing in one of the UEFA competitions, had to be given byes through the Intertoto knock-out rounds (until they were eliminated from the UEFA competition), or withdrawn entirely.
This made the knock-out rounds complicated, difficult to schedule, and weakened their significance.
While reaching the final was seen as an achievement worthy of praise, the main purpose of the tournament, for most clubs who entered, was to provide football during the otherwise empty summer break.
Having to arrange and play home-and-away knock-out matches during the new season was seen as difficult, expensive, and relatively pointless if the club in question was eliminated before reaching the Final or Semi-finals.