With a 250,000 instance dataset I'm seeing these problems with the dataset tools:

Takes a long time to load a dataset
Takes a long time to submit an edit, even if that edit is just to make ds public
List of instances in a class (on edit and view) is not paginated, so this page takes a long time load, or doesn't, depending on how many instances
Evaluating a dataset times out because validation checks that each mbid exists in the lowlevel table.