I suppose it’s the same as cooking your own food, rather than getting a takeaway – you know what ingredients went into the dish.
If you add the lines to your functions template, you have guaranteed the correct version of jQuery is loaded for your theme. If you rely on a plugin and you distribute your theme, the results may vary – if the end user doesn’t have the same plugin.
On the flipside, the plugin may be well maintained. Updates could be automatic, in a set-and-forget kind of way.
c2k
