I agree with hixxy regarding font locations. Fonts have almost always been in either a View menu or a Format menu. It would be highly unusual to find them in a Preferences or Options dialog. It makes sense to have them where they are. In addition to there, you can change them on a per-window basis from the window's right click menu, which is also intuitive once you know there is a right click menu there (of course, knowing about the right click menu may not be as intuitive as it could be). The choice of font as an example wasn't a good one because it really does make sense where it's at.
That being said, other items could be more clear for a new user. Khaled is already trying to push for that by limiting new options and reducing the number of options available in the dialogs. He's been pushing back lately against requests for additional options for that reason. But that's only partially helpful. It would help to rearrange some things and place them in more natural locations. Having to go to multiple locations to adjust DCC-related settings is far from intuitive, for example.
If nothing else, it may be a good idea to adjust the default settings to something a new user with little to no experience with IRC would want. In addition, to provide a short setup "wizard" to set up the main items such as nick, network(s), and channel(s). That would get a new user to the point where they shouldn't have to really adjust anything to use mIRC until they are ready to start playing around with the settings.