It's reliance on google's protobuf with it's 2gb single file limit is an extreme limitation. Yes you can keep weights outside your model file, but still many operations (model slicing) fail.
Second, inability to offload parts of the model to disc or cpu(like huggingface accelerate) while the rest executes on the gpu.
Thirdly, inability to partition existing large models easily. You can delete nodes, but then fixing the input/output formats means manually editing text files. The work flow is ridiculous (convert onnx to txt with pdoc, edit in text editor, convert back to binary).
I really wish they fix all this stuff and more.