That would indeed be an awesome function, I have troubles as well with plugins that don’t recognize the caching W3 cache plugin. Guessing this might be hard to accomplish though.. hoping for answers… 🙂
I think you don’t need this if you disable the page cache (overall cache) and just enable the DB cache + object cache. Having used HyperCache that had such a feature, I realized it was not very effective from a maintenance perspective over time. Just write your code as you would write it, don’t tailor it for a caching plugin! W3TC is already fairly savvy for advanced websites with its DB + Object cache.