Extensions can do a heck of a lot. Since the system is still under development, new (good) ideas would likely be welcome. Mozilla integration, for example, is a bit loose. To get certain signals from Mozilla, you may have to hack at files within the epiphany/embed/ directory in the Epiphany source code. If your patch is clean and logical, submit it to GNOME's Bugzilla and you'll have a good chance of its getting applied.
Stylesheet manipulation is one very important missing feature (all the more important because Mozilla Firefox's extensions are so powerful in this respect). At the time of this document's writing, the author is hacking at Epiphany to improve CSS manipulation from within extensions (and Epiphany itself, for that matter).
Are you an uber-hacker? Here are some challenges. Note: very possibly, a perfectly acceptable patch would not be applied to the official Epiphany source tree. Consider discussing on developer communication channels about how you would modify Epiphany; you will probably get some helpful advice.
A JavaScript extension system similar to Firefox's: this would naturally be integrated much more tightly with Mozilla, and loosely (if at all) with the Epiphany UI.
Note: Some such JavaScript-heavy, UI-free extensions actually work fine with Epiphany already (flashblock is one such extension).
A C# extension loader. The epiphany-mono directory in GNOME CVS has the beginnings of such a system. There are a few bugs, and there is no documentation (this document, for instance, should be updated to include C#).
[Insert your favourite Firefox extension here. Then make it better.]