I have a page with a lot of text and descriptions and screenshots covering both.
http://www.natami-news.de/html/support.html(still in development :-) ).
To answer shortly... I use it emulated on a fast PC so I cannot compare it. Amikit has more features/preinstalled software and is really nice but also needs a lot of resources (I think 68060 and graphic card and more RAM recommended). AmigaSys is more lightwided and there also exists a AGA-Version, so without graphic-card I would prefer AmigaSys. For those who want the "3.1."-Look I would recommend BetterWB.
P.S. I overread that you want AmigaSys or BetterWB. "Better" is relative, BetterWB is lightwide and does not change anything at the user interface (just modernize and add programms and patches), AmigaSYS is offering a rich-gui with preinstalled software and a better and more attractive user-interface.
I have none of theses installed on "real" hardware so I cannot say much about this. Propably you need a clean install. They should both run on your system.