The Global Computer Environment (GCE) has become the basis for increasing the size of large distributed systems with control. The conditions for their growth are determined by the positive synergy of the network effect according to Metcalf's law. The paper shows that heterogeneity is the main source of negative GCE synergy. Excessive growth in the cost of distributed systems is associated with the combinatorial complexity of the functional integration of initially heterogeneous network resources. Heterogeneity and intra-system imbalances of GCE development activate secondary sources of negative synergy. The paper presents an original approach to studying the fundamental intra-system regularities of GCE development as an integral object. - For the first time, the ways to eliminate the GCE intra-system negative synergy are shown, which open up opportunities to minimize the costs of creating and developing arbitrarily large distributed systems in GCE.