1. You don't really care too-much about accessing subsets of columns
2. You can't easily append stuff to closed Parquet files.
3. Batched-row access is presumably slower due to lower cache-hits.
It's okay for map-reduce style stuff where this doesn't matter, but in ML these limitations are an annoyance.
HDF5 (or Zarr, less portably) solves some/many of these issues but it's not quite a settled affair.