Maptool has the best vision, lighting, and FoW system of any VTT. It is very flexible and powerful in that respect.
OTOH Maptool's macro facility is pretty arcane. Making simple macros and basic tracking of character attributes is not hard, but more complex stuff is not at all straightforward. It is QUITE powerful and people have written entire macro frameworks for 4e that do a lot of cool stuff. However getting stats into the proper format, tweaking macros to deal with all the little idiosyncrasies of 4e powers and whatnot, etc is a bear. You can use something like Rumble framework, but there's a pretty good learning curve to setting up PCs and monsters the way you want them to work.
I think Maptool really IS the clearly best VTT out there, but there is a good deal to be said for the greater ease of adoption of some of the others. FGII for instance IIRC has a pretty good 4e plugin. It can't do everything Maptool can, but OTOH you can get up to speed quicker. I've only used it a very small amount though, so I am not really the best judge of that.
Another advantage of Maptool is simply that it is Java and thus you won't have all the issues with getting everyone up on it on Macs and other systems (I run Linux for instance, you simply cannot get FGII to work reliably).
