>Admittedly, I didn't know whether L2S would generate 2000 code - I haven't used 2000 in a long time. However, I DO know that until a new client is released that supports things like the new HierarchyID data type in 2008, people have to wait. So unless the day comes when both products are released on the same schedule, L2S will always be in some deficit position when it comes to supporting the newest database language features. That in itself is a major issue.
I just got a pointer to this blog
http://ayende.com/Blog/archive/2008/10/31/microsoft-kills-linq-to-sql.aspx
If it's not broken, fix it until it is.
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