I will confess that one feature I’m missing in Scrivener is regular expressions, both for searching and for search/replace.
If Scriv 3 turns out to incorporate a regexp library (ideally PCRE (http://www.pcre.org/) I’d just about keel over in ecstasy.
(Note: regular expressions or regexps are the grown-up version of the primary-school pattern matching you get in MS Word’s advanced search and replace. PCRE is an open source library based on Perl’s regexp capability, which is about the most monstrously powerful implementation of pattern matching there is. PCRE is distributed under the permissive BSD license, so: “The PCRE library is free, even for building proprietary software” (per the website). What I’d like to see is simply a preference somewhere to switch from the usual search library to PCRE for “advanced” searching. If this is feasible …?)
That’s definitely on the list, along with general improvements to project searching (potentially multi-axis and whatnot), especially now with 10.7+ adding NSRegularExpression (ICU based; I would prefer PCRE as well as Perl is what I grew up on, but ICU has much better Unicode support, and is based on Perl syntax so there isn’t a big learning curve), it shouldn’t be difficult to provide.
Regular expressions are a dark art, best left to those with the twisted minds of the dread vi user. Seriously, there’s an entire O’Reilly book on it. I only ever read chapters one and two, and am considered a regex guru among my coworkers. Of course, they use ftp programs to bring unix scripts to their Windows desktops and edit them in NotePad …