It would be great if AppInsight for SQL could be configured to ignore small indexes for fragmentation. Indexes with only a few pages are likely to be fragmented and there is nothing you can do about it - nor is there any real performance impact due to their small size. I would love for you to be able to set a "Number of pages over XXX" to be eligible for monitoring. Without that and the ability to ignore certain indexes that will always be very fragmented (somebody else already submitted that idea) we aren't going to be able to get much benefit from the index fragmentation portion of the AppInsight for SQL.
