I'm not qualified to give a complete answer, but I think two main issues are the proliferation of flags in standard tools (e.g. ls has a lot of flags for sorting behavior) and the extreme preference for plain text. Text is very useful, but a lot of semantic information gets discarded. Representing structured data is painful, stdin/stdout/stderr are all in one place, window resizing makes a mess sometimes (even "write at end of line" isn't given), and so on. I'm definitely not qualified to describe just how to fix these issues, though.
raddan|1 month ago