The problem:
Typical URLs on PHP-using sites differ mostly by parameters, so any
"indexname.php?parameter=XYZ" (date, page, etc) ends up mirrored as
"indexnameABCD.html", with internal links having purely decorative
"?parameter=XYZ".
Since the real URL in the archive is unpredictable, this makes navigation
possible only via mirrored links. It's fine if there's an extensive index, but
some sites (like webcomics) have little but "back" and "forward".
This also seems to cause troubles when updating, but i'm not sure.

Proposal: an option to convert such URLs into
"indexname.php&parameter=XYZ.html" instead - this would make mirrored URLs
corresponding 1:1 with the original in a clear and predictable style.

If added as an option, this feature won't cripple the overall useability in
any way, user just won't enable it for sites messing up the order of
parameters or doing anything else that would create near-endless duplicates.
This still leaves the possibility to add later things like parameter sorting
and ignoring junk options like sessionIDs.