In version 3, I have an annoyance where I'm using the Jinja2 HTML templating highlighting plugin, but also get suggestions for various PHP completions, which are completely inappropriate. At the same time, I can't take the PHP support out of the default HTML package without breaking PHP highlighting completely.
My suggestions is to split HTML highlighting up into a "base HTML" highlighter, which only does actual HTML (and probably CSS and JS), and then extend it with the appropriate scripting/templating languages as needed. I haven't studied Sublime's highlighter interface in detail, but as far as I can tell it should be possible to do.
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