The query optimiser hotfixes contained under Trace Flag 4199 are intentionally not enabled by default. This means when upgrading from SQL Server 2008 R2 to SQL Server 2012 for example, new query optimiser logic is not enabled. The reason behind this according to the article linked above is to prevent plan changes that could cause query performance regressions. This makes sense for highly optimised environments where application critical queries are tuned and rely on specific execution plans and any change in query optimiser logic could potentially cause unexpected / unwanted query regressions.
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