I can only think of having "02" instead of "2" and so on.
..It would look ugly though IMO, and it would require tons of re-tagging for my collection...
I think it's the best way. It needn't look ugly when playing as the WPS can display the metadata almost any way you like. The track numbers aren't part of the title metadata, even though they are useful in a file name. In any case the CD track numbers are a convenience for the medium, not part of the work; this is especially obvious in long works where the track numbers are merely index points in a long uninterrupted performance. So the metadata on my collection mostly looks something like:
$ mediainfo 05\ -\ Out\ of\ the\ deep.flac
General
Complete name : 05 - Out of the deep.flac
Format : FLAC
Format/Info : Free Lossless Audio Codec
File size : 23.7 MiB
Duration : 5mn 58s
Overall bit rate mode : Variable
Overall bit rate : 554 Kbps
Album : Choral and Organ Music
Track name : Out of the deep
Track name/Position : 05
Performer : Oxford Camerata & Jeremy Summerly
Composer : Orlando Gibbons
Genre : Early
Recorded date : 1994
Comment : Laurence Cummings, organ
The filename contains the track number so it sorts properly in a file manager or file name based player, and the tag contains a track number formatted to sort properly in a database based player. Neither filename nor track number is of much interest beyond that so
in Rockbox on my player with a custom WPS it will look like so:

Naturally where tracks are named by movement/part number then that is part of the title of the work, so is written into the title tag and displayed.
For classical music it's a good idea to customise your wps as well as your tagnavi tag search format. That frees you up to make full use of Composer and Comment tags, which in turn lets you use Artist/Performer and Album tags in a sensible way (like for the performers and the album name!), and you can finally forget about trying to mangle file names into poor man's tags.
The options for WPS are great. You can have alternating fields, conditionals, controllable scrolling, choice of justify left/centre/right and so on. Some reading and probably some trial and error and you can have everything look nice and also display everything useful without looking too fussy or crowded.
I don't know what tagging apps or tools you prefer but some of them make automatic renumbering and other batch operations very easy. The most appealing method is to script it but if you have numerous different file types and/or inconsistent numbering and naming schemes it could be tricky.
It is definitely worth having everything numbered in a way that works as expected on every different OS, file system and device. The alternative of waiting for all the different projects and people out there to change their apps and devices to a numbering scheme that they don't want to use is a bit of a long shot. It might be a big and quite tedious task but once done it makes it very easy to switch devices, formats, operating systems, applications etc. without it becoming a big deal. It's also the kind of task where you get the opportunity to fix all the other crap you find along the way......