Hi!
This depends on your algorithm) Explore, what it does and what Revit does extra? May be you should divide document modifications to multiple transaction, may be vice a versa union transaction in one big transaction.
I've faced with the same issue when my addin needed to create multiple detail lines. Revit automatically attaches the end of line to the point of another line if the first line ended at the second line. For few number of lines it does not matter, but the time and consuming memory grows exponentially when lines number increases. Firstly, I've reduce the number of lines, that addin creates, secondly, I splitted lines creation to multiple transaction.
