Alliances form because organizations have similarities, and commonalities that promise synergy.

However, most alliances fail because they fail to manage the areas if dissimilarity.

Leo Tolstoy  remarked that happy marriages were the result of the manner in which partners dealt with incompatibility, not how compatible they were.

It is the same in a commercial alliance, the literature is full of examples of alliances of one sort or another that emerged because of the prevailing logic of moving into adjacent market areas by merger or take-over, based on seemingly common customers, technologies, channels, or philosophies, only to find a disaster waiting because they failed to see how some  dissimilarity that had not been considered relevant threw a spanner in the works, and cost the alliance. 

After the synergies have been identified and quantified, but before the deal is done, have a separate group look for the areas where there are no synergies, where the organisations differ substantially, and assess their impact on the potential for disruption of the alliance working as well as the optimists predict.