This is more a general statement, keep in mind it has been almost 25 years since I used ME.
More it was at the mercy of the software industry of the time. Development of complex utilities from video editing to web browsers being more than just HTML viewers and fighting over limited memory trying to manage a high stack of rapidly more complex drivers and ME just didn't handle it that greatly. The modem, printer, high end GPU's and audio systems all fighting to work together.
It just seems like the whole Windows system pre-NT was struggling to stay together. Cue the famous Win 98 demonstration crashing the system via a Plug and play scanner. Win 98 SE was in a bizarre stable state, ME wasn't and the differences under the hood could have been something that appeared fairly minor.