Just encountered this for my first time. I didn't really have anything useful I could aggregate or group by, as the intention of this chart was to show as much data as possible. So, I created something which would group them together only when necessary, keeping us below the 1,000 data point limit at all times.
Create some hidden data, and use the following:
ROUND(RANK(A:A)/CEILING(COUNT(A:A)/1000),0)
Group on this hidden data.
where A:A contains unique identifiers for your data.Now, the number of data point will be 1:1 up to 1,000, at which point they are grouped in pairs, then triplets etc, maintaining the maximum amount of visible data all the way.