I'm not totally sure what you're worried about, but I think this will clarify what JQuery UI does and does not do for you.
"Ready for prime-time?"
Yes. The JQuery UI themes have been around a long time and have no screaming-to-the-surface-to-ruin-the-project issues. There are some known issues, mainly with advanced CSS3 issues. For example: All browsers except IE6 have rounded-corner support from CSS3. JQuery UI themes use this feature. If you want rounded corners in IE, you will have to get an extra plugin that works around it for IE, specifically. That's easy enough.
The non-obtrusiveness of JQuery themes is easily assured, because the themes stay separate from most of your site-specific design concerns. The classes implemented by the UI themes mean things like, "this is what an active thing looks like." Tweaks you make to such general concepts tend to be small ("3 shades of pink lighter than before") and usually don't change dimensions very much ("add a little extra padding to active things"). Plus, to do all that, you can use Themeroller.
Using JQuery Themes
The nice folks at Filament Group have a nice write-up on how to style things using the JQuery UI themes. I don't think I can add much to their walkthrough of it, except to point out that they are using both a garden-variety JQuery theme and their own layout CSS. This is all about the separation of theme vs. layout.
Themes vs. Site Designs
It's very important to remember that themes aren't layouts. There's a huge difference between them. JQuery Themes do a good job of staying on one side of that fence, and by that virtue are non-toxic, easily-replaceable additions to a website. Consider:
Layouts are pretty hard, and include stylistic decisions which are nontrivial and site-specific. Examples of design questions include:
- Where does that button go?
- How big should menu buttons be?
- Should this table be centered?
- What font size do I want in the menu buttons?
Basically, you always write your own design. If you've taken one off the shelf, you're either planning to modify it heavily, or you're building a very cookie-cutter website.
Themes, such as JQuery themes, give an overall look and feel to your layout. They can be independently swapped out, added later, or whatever. Themes are, at some level, the difference between 1) a good interface or 2) a good interface that is also attractive and consistent. Theme questions include:
- How does clickable button look, usually? What about a disabled button?
- What color is everything, in general?
- How round should box corners be, in general?
- What is the general font size and color?
So, once you look at a theme on one website, you can probably take the same theme and apply it to your own very unique site design with only small differences. They should be totally benign.