Ok, no one got back to me on this and I was finally able to pinpoint the problem. It's definitely an issue with SQL Server 2012's version of the data collector warehouse DB schema (as of version 11.0.2325 at least).

I compared the schema of the 2008 R2 and the 2012 warehouse databases. I found out that the snapshots.rpt_query_stats procedure definition has changed, for the worse.

If you look at around line 73, you'll see that the FROM definition changed

SQL 2008 R2

FROM snapshots.query_stats AS stat

SQL 2012

FROM

(

SELECT *, DENSE_RANK() OVER (ORDER BY plan_handle, creation_time) AS plan_number

FROM snapshots.query_stats

) AS stat

Cost of query relative to batch in SQL 2008R2 is 57%.

Cost of query relative to batch in SQL 2012 is 100%.

The results of this is that when I click on a query in the query stats report to get the detail information, the query that took only a few seconds on my 60 GB SQL 2008 R2 database now takes about 8 minutes on my SQL 2012 database. Even when I reduce the data retention to 3 days dropping the database size to about 10 GB, the query is still taking 1.5 minutes.

Can someone please confirm my results?

Can someone also please tell me how to get this reported as a bug for 2012? (or if it's already reported as a bug)