As you noted, iUI's transitions are not really usable. But the deeper
problem is that iUI's stylesheets and code depend on the DOM structure
being exactly as they are in the iUI demos. If you start adding
elements like headers or footers, things break. Like iUI wants things
in HTML > BODY > UL and things break if you have HTML > BODY > DIV>
UL.

There are various forks of iUI and libraries "inspired by" iUI that
are probably more appropriate. Unfortunately, it is kind of the wild
west out there with various libraries each doing 70% of what the other
libraries do, so it's hard to point to a single one and say: "That's
probably what you need." New libraries sprout up more quickly than
anyone has an opportunity to evaluate them. There is a list here:

PhoneGap-compatible Javascript frameworks:
iUI - make iPhone-feeling interfaces
xUI - slimmed down jQuery work-alike
Magic Framework - make fast and smooth iPhone-feeling apps with
native-feeling widgets, lists, etc.
Dashcode - Framework from Apple
JQTouch - JQuery Plugin for Making iPhone-like apps
CiUI - CNET iPhone UI
Safire - Zillow JS/CSS framework (MIT License)

http://phonegap.pbwiki.com/