Re: how much of the style will change in future upgrades
Just curious why you prefer jquery vs prototype? Personal preference or do you see more options with jquery?
"Secretstache" & "Mememe" said it all

. Also there is more Jquery are pre-included with
WP.
http://codex.wordpress.org/Function_...enqueue_script
I just started playing around with
WP a months ago and not sure how everything works but seems like you better use this wp_enqueue_script if you wants to build higher quality theme.
http://www.prelovac.com/vladimir/bes...rdpress-plugin
And just for confirmation, For now i only found 3 areas that are using Prototype,
1. "Post Classified" - toggle
2. "Contact Ad Owner" - toggle
3. LightBox
I haven't search all so not sure...
Can I ask how as I need to use JQuery for other custom functions plus I prefer not to use Prototype.
Sorry i am not sure what do you mean. Can you explain little more? (My first language is not English, apology

)