Question : sys.indexes vs sysindexes

what specific disadvantages of sysindexes has sys.indexes overcome in the newer versions?

there is a lot less records in sys.indexes.

Answer : sys.indexes vs sysindexes

Use sys.indexes for SQL Server 2005.
sysindexes is provided for backwards compatibility

refer this article for getting the entire list of new system views that correspond to old system tables
http://msdn.microsoft.com/en-us/library/ms187997.aspx
http://www.sqlteam.com/forums/topic.asp?TOPIC_ID=107385
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