I've added two Web Inspector capabilities to weinre, hopefully these will help.
1) When you reload a page with the weinre client still running, instead of getting the collapsed <html> element, you should get what you got the first time - nodes expanded thru <body>. In addition, if you've selected an element in the element pane (click on it), the last selected item before you reloaded should also be expanded out.
2) When you call the inspect(thang) function, from the console, where thang is a DOM element, that DOM element should be expanded out in the element pane. Note, I believe you can only call this from the console, not in your code. Seems like it would be nice to have this available as a function on console as well.
I think 1) will work out well, since you don't have to do anything special - kinda does what you'd hope it'd do. The second may work out well if you have easy access to your elements. Keep in mind you can use the "command line API" functions like $() and $$() with inspect().
You can try this out in a build I just did, located here:
You can npm install via:
sudo npm -g install http://people.apache.org/~pmuellr/weinre/builds/2.0.0-pre-H1FFX7OT-incubating/apache-cordova-weinre-2.0.0-pre-H1FFX7OT-incubating-bin.tar.gz
Let me know how these work out. If the console.inspect() function sounds interesting, so you could (temporarily) add it to your code, let me know and I'll open a bug against Big Web Inspector (and add it to weinre straight away).
I'm open for other ideas. I like the idea of "bookmarking" elements, kinda like Watch Expressions from the Scripts Pane, but for the Elements Pane. I'd rather inherit that code from Web Inspector than write it from scratch tho