• slow parsing of big xml files
• outdated and incomplete function list
• inconvenient customization
• ignores current context/scope (namespace, class and etc.)

I suggest adding support for custom/user auto-completion adapters.
simple solution is customization by autocompletionAdapters.xml file:

<?xml version="1.0" encoding="UTF-8"?>
<NotepadPlus>
<AutocompletionAdapters>
     <!-- 
     name: adapter ID
     language: NPP language name
     command: pattern CLI command, placeholders
         $(WORD) text to search
         $(FILE_PATH) full path to active file
         $(LINE) current line
         $(COLUMN) current line position
     bgcolor: optional background color of adapter's items in autocompletion list
     -->
    <AutocompletionAdapter name="php7" language="php" command="php -f nppAutocomplete.php $(WORD) $(FILE_PATH) $(LINE) $(COLUMN)"/>
</AutocompletionAdapters>
</NotepadPlus>

Adapter command must return XML with custom list:

<?xml version="1.0" encoding="UTF-8"?>
<NotepadPlus>
<AutocompletionAdapterResults>
     <!--
     value: autocompletion value to insert
     label: optional label display in list instead value
     hint: optional hint/description
      -->
      <AutocompletionAdapterResult value="..." label="..." hint="..."/>
     <AutocompletionAdapterResult value="ClassName" label="Namespace\ClassName" hint="Internal PHP class"/>
     <AutocompletionAdapterResult value="ClassName2" label="Namespace\ClassName2" hint="Extend ClassName class"/>
     <AutocompletionAdapterResult value="ClassName3"/>
</AutocompletionAdapterResults>
</NotepadPlus>