After the performance improvements from T121901 earlier this year, we can probably increase the number of uploads allowed at once (maxUploads), currently set to 50.
I'm not sure how far we can bump it, but we could probably do 500 easily and then maybe try 5000, which should be enough even for mass uploads.
We'll need to test stuff a bit, verify that things are not taking unbearably long, verify that we're not using unreasonable amounts of memory with this many files, and verify that we're not doing something accidentally quadratic on the number of uploads.