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What are the pros and cons of using the BCS to integrate an external system into SharePoint versus a custom integration.

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You will find a discussion here: layer2.de/en/community/FAQs/BDLC/Pages/… Think its not about "custom" only. Possibly a 3rd party app can do more compared to OOB BCS, especially with SharePoint 2013 or SPO/cloud. 3rd party tools avoid programming, and can offer all native list features, e.g. search, change notifications, workflows - not only displaying external data on SharePoint surface... – SharePointFrank Dec 4 '12 at 12:59

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Pros

End User

  • Business Data Web Parts & External List can render data out of the box
  • Enterprise & FAST Search Integration with Managed Property Mapping support
  • User Profile Synchronization
  • Office Integration via External Data Column
  • Office Mapping for Tasks,Contacts and Calendar
  • SharePoint Workspace Support
  • Single Sign on Support
  • Workflow support via External Data Column and External List

Developer

  • Visual Studio Tooling Support
  • SharePoint Designer Support
  • Out of the box support for existing SQL Databases & WebServices
  • .Net Assembly Connector can connect to any other datatype
  • Server side API to develop custom web parts against
  • Client Side API to develop custom client integrations against
  • Write once work against any data source controls are possible

Cons

End User

  • Out of the Box Web Parts look outdated
  • External Data Column data needs to be refreshed

Developer

  • Generation and Maintenance of Model file is time consuming.
  • Data Model does not support subclassing.
  • Writing controls that work against any data source is time consuming.
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Fabian Williams had a related post about the topic (BCS vs Alternates) a few months ago - http://www.sharepointfabian.com/blog/Lists/Posts/Post.aspx?ID=202

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