Running BGP between the links has several advantages. Your IGP does not need to carry unnecessary routes from other regions, so regions can grow independently. Problems within a region are confined to the local region only, which offers a lot more policy control.
Also, consider the current trends in the industry. In today's fast-paced market, many large companies are acquiring other companies or are merging to compete in their respective markets. With mergers, another complication is added to the network—merged companies usually have not been running the same IGP. For example, one organization may be running OSPF, and another may be running Enhanced IGRP, so they must accommodate each other and re-engineer the new network to run a common routing protocol, or redistribute between the two. This extends the boundaries of the IGP.
Secondly, not all operations are placed into one administrative control immediately. Even if both organizations are capable of moving their networks into one IGP, an important question arises: What happens when this newly merged company buys another organization? Clearly, adding another iGp would create immediate problems which can be addressed only by running BGP between the links.
To summarize, a BGP core between regions prevents unnecessary flooding on costly links, simplifies the merging of organizations, and offers greater policy control.
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