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Structured Maker is an excellent tool for authoring and maintaining XML files, IMO. There are people who would disagree, but I haven't seen the problems they mention. Or rather, I see the same problems in any other product -- namely that you have to map the XML structure to some form of rendering, and that is never free (except for XHtml in a browser). It boils down to how each product accomplishes this mapping, and what that product gives you out of the box so you can get started. So really, what you're asking is, "For the way FrameMaker achieves this mapping, what do I have to worry about?" If all you're interested in is using Maker's structure WITHOUT mapping it to XML, then you have no question to ask... And yes, there are use cases for this.
Any mapping issues come from the fact that the FrameMaker document model preceded Maker SGML/XML support. So it takes some wrangling to render some constructs. Tables are an obvious area. Maker cannot make tables within tables, but XML can. So you definitely can't render that. More generally, the CALS table model is usual in XML. Maker knows how to map to the CALS model, but you have to be a little careful with your attribute and element naming on the Maker side. If you use the same names as the XML you should be fine. Look in the Structured App Dev Guide for more details.
Another area is mapping xrefs and index entries. In Maker these are markers. Default mapping usually works, but you have to be aware of this.
Finally, graphics -- for example, if you draw graphics in your Maker files (say, add callouts in Maker), then when you save to XML that gets converted into a binary image. So I tend to just handle images outside of Maker and import them.
Maker provides out-of-the box support for some standards -- DITA and DocBook. I know next to nothing about DocBook. I've been using Maker with DITA and not had insurmountable problems. It's excellent for authoring because I can see what my PDF output will look like as I go. And it's excellent for generating PDF. I use in-house processes to generate HTML help out of my DITA source (not OT -- I generate the HTML on the fly per browser request).
You can also look at Leximation for valuable DITA enhancements.
Hope this helps...
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