I am finding that metaPDF is quite slow in general but it is grinding to a standstill when I try to highlight text. I am not 100% certain it is the highlighting causing the slowdown or if that is coincidental. I get Chrome's "Unresponsive page" box at some point whenever using metaPDF.
In this instance the document is 15 pages and the file is 2MB.
I can appreciate that it is very difficult to diagnose these issues without a lot more detail on the specific context - is there a way of producing log files that may be helpful to you in diagnosis?
The only comparison I've got is that I can open the same document and annotate it in PDF-Xchange and Xodo.
As neither of those automatically sync changes with Google Drive, relying on manual saves, I turned 'Auto-save' off in metaPDF case that was the cause of the problem. metaPDF became more responsive initially, but it was still much slower, stuttered and eventually resulted in the "Unresponsive page" message.