Territory Security - the current implementation makes it impossible for a salesperson to work on an entire account (parent in one territory, offices in another territory) when you have one Salesrep per territory and are trying to protect your overall account base from being stolen when one disgruntled salesrep leaves - for example that is.
Plus it has other limitations when working with national accounts and international customers, or working with BAQs and Dashboards for summary information, pipeline reporting, etc.