I just read this series. I'm glad I did too, although it's kind of all over the place. What I really enjoy about it is that it's obvious that both the artist and the author [well at least Nisio] are having fun with the series. It's all over the place, it makes very little sense but it's very entertaining, quite funny and vividly captivating.
In terms of arcs or sagas, I do think the Zenkichi vs Medaka one [ie the most recent one] was my favorite, not just for the fourth wall being obliterated or the meta-ness, but in terms of an actual story or character development it was a great final arc. The SoL arc was quite timid, the shonen battle saga, ie the enforcer arc and the class 13 tower arc, was alright, not really my thing, the Psychological battle Saga, aka the Minus arc, was excellent and the fake Trick Tower arc was pretty good. All in all, a pretty good series, and I hope this new arc will be just as good. I would say Zenkichi is going to go and become Medaka's suitor, but that's a bit too lame for this series I think. Either way, I really do hope this series ends soon, it doesn't really have that much else to go on.
Now my only assumption as to why it didn't finish was that the editors wouldn't allow him to, or he just wanted to troll everyone. Both very likely.