It'd be good to at least have original published order in the metadata. For chronological or suggested reading order though, it'd be better if publishers maintained a wikipedia page or similar listing on their own sites as that order can change as new books are written. That'd be asking too much though
Until then, using calibre is really the best answer.
With calibre, it's dead easy to set the series and number just type "Name of series [x]" in the series field, replacing x by the number you want. Also, you can setup a plugboard for save to disk and send to device that will rename the file so that it appears on your device with "series name - 01 - book title" or whatever variation of that you want.
If you want to set calibre up to do that, have a read about plugboards then setup a template with the following replacement for title:
Code:
{series}{series_index:0>2s| - | - }{title}
Ideally what I'd like to see is an official series name and published order entry in the book metadata. In addition, make reading order and chronological order entries an optional part of the standard. Then devices can rely on those entries (when present) to provide additional display/sorting options for books with a series. It can be left up to the reader if they want to set/update the chronological/reading order for their books.