In essence, megaregions are a kludge, and I've certainly called them that before myself.
As I understand it, OpenSim can easily be configured for variable size regions, but the viewers can't handle that, so megaregions were attempted as an experimental work around.
When I first tried them they were more trouble than they were worth, and other people were finding that too. Definitely belonged in the technical category "kludge".
They improved then to the point of being quite usable, but still having some awkward characterisitics and limitations and still being kludgeworthy.
Now Kitely have their advanced megaregions and their own asset service, things seem to work better there. Also I believe they've improved megaregions and OAR options in standard OpenSim. A lot has happened in the last 12 months, and I haven't got around to testing the recent versions properly. I still wouldn't disagree with anyone who called megaregions a kludge, but I would say they're working pretty well now, and anyone basing their opinion on earlier experience should try them again. I expect there's a lot of mainstream software with features that started as hurried kludge and are now integrated to the extent that most wouldn't notice.