sorry for the long delay in answering and thanks everyone for all the hindsights. The link given by @dgault in Bio-Formats ome-tiff write time issue / bug? contains references to some writing performance improvements change that have been recently proposed by ourselves and contributors.
Although these changes have given us substantial writing improvements in our recent testing use cases, largely using the Bio-Formats command line tools, it does not address the speed of writing OME-TIFF using the ImageJ plugin in the conditions described above.
We believe the issue discussed in this thread is specific to the usage of the writing API in the ImageJ plugin. As we have now completed a large portion of our work on pyramidal OME-TIFF (watch https://blog.openmicroscopy.org/ for more information), tackling this performance issue is now part of our outstanding and immediate priorities.
For developers, you can track the latest progress on the dedicated reference card - https://trello.com/c/Qk6NBnPs/92-imagej-ome-tiff-writing-performance. Once we have a fix ready to test by the community, we would propose to enable development milestones of Bio-Formats 6 via the development Bio-Formats update site.
Sébastien, David, Melissa & Josh