well since you asked.... 1. make all common templates & extensions interchangeable in a manner like the media from $wgUseInstantCommons = true;. i.e write or update & they work in all enabled sites like photos do. 2. be able to set all scripting languages to be used as needed in a manner like $wgScriptExtension = ".php"; $wgScriptExtension = ".lua";$wgScriptExtension = ".js";$wgScriptExtension = ".pl"; 3. Do away with external extensions for scripting make mediawiki aware of and able to use any installed scripting language.
I'll likely think of more but for now these would be welcomed changes.