Basically, the client-side autoexec files are good (a godsend compared to the old way where you had to toggle through maps/teams/etc), but they have some deficiencies. No doubt per-weapon scripts have already been mooted, but a less obvious one is per-mapSCRIPT.
It's only really likely to be an issue when making spawn scripts etc - where it's common for map scripts to add/'move' a spawn - changing the order and numbering of the spawn points, and hence requiring a new mapscript. Except you can only have one script installed for each map.
My suggestion to kick things off: leave the current naming conventions intact, but if a file '/etpro/autoexec_MAPNAME.MD5.cfg' is available (where 'MAPNAME' is the .bsp name, and 'MD5' is a hash for the mapscript), exec that as the per-map file.
Not sure if it'd be more hassle than it's worth (mapscripts are _normally_ put in pk3's by server admins which get downloaded - but I am aware that you can just leave an edited mapscript on the server, and I'm not sure if clients get that script... guess they must... so they can compute a hash), but any thoughts/rage?
