Current messenger stand alone app definitely. However, wait till April when this app along with new Facebook app will integrate much better than we have in built now.
You have to realise that current integration is redundant now. Why? Because it supports messenger chat and facebook chat. Now messenger does not exist. There is no way you can add friends to messenger. You can't make new friends. With Facebook chat - it lacks features. It doesn't allow sharing of photos, videos, voice calls, stickers, viewing last seen status, viewing "typing" status. Why does it even make sense to stick to integrated one?
WP8.1 will let other apps hook into the system apps - that is far better. You can have a choice of Skype, Facebook and hopefully Whatsapp - to hook into messaging hub. Far superior than our current integration. This way you will be able to enjoy all the facilities of apps right from your messaging hub. I have stopped using integrated chat and social network share and rather use the apps now. Yes, I am all up for WP having its own identity as "integrated around people" - but current integration is far too limited, lacks features and redundant. If what they are doing with WP8.1 brings more features, more apps to integrate and more stability, why resist?