We have performed a multitude of upgrades from SQL 2000 to SQL 2008 R2 (and still habe many more instances to go).

The issue you are experiencing performance wise we uncovered in testing upgrades. This type of performance degredation was uncovered in less than 5% of our upgrades.

Our solution was to drop all 'system generated' statistics right after the upgrade prior to:

- 'update statistics' (with full scan)

- defragment all non-clustered indexes

- defragment all clustered indexes

and we added:

- 'refresh' all views (basically sp_refreshview for every view in the database)