I do agree with the markup problem... they should be using much more CSS than they are.
In fact, I would make a bet that it's possible to do a site layout where switching the stylesheet changes the layout of the posts from their 2D format, to the 2chan-style layout, to the LiveJournal/Slashdot style threaded layout, and so forth. All it needs is a bit of ingenuity and tricks with CSS tables. :-)
The other problem I have with the site is that it's an app made in 2006 and it doesn't include any AJAX features. 4-ch is excused from not incorporating AJAX because it's relatively old... although it would be a nice feature anyway. ;-)
The tripcodes seem fine though... I don't know what you're talking about. The only limitation is that it doesn't let you have a tripcode and no name, but that limitation kinda makes sense anyway.