Mega-exo is theoretically is supposed to last longer, but they have had problems with cups loosening. The bearings are larger and cheaper to make. they actually drag more than simple square-tapers (this month's velonews test).
ISIS can be built lighter. The problem with ISIS early BBs is that the bearings wore out quickly due to the small bearing diameters and good ISIS BBs were expensive.
Newer ISIS BBs are very reliable. I use a Token ceramic bearing ISIS with Ti axle.
ISIS Drive, the International Splined Interface Standard, is an open standard splined specification for the interface between a bicycle crankset and the bottom bracket spindle. It was created by King Cycle Group, Truvativ, and Race Face in response to the proprietary Shimano Octalink splined bottom bracket standard. Because the Shimano splined interface is covered by patents, the ISIS Group created the standard and put it in the public domain so that other companies could make interoperable components.
MegaExo is similar to Shimano's outboard style bearing BB interface and is an FSA patent. Same principle, different name. Outboard style bearing is said to prolong bearing life because the wider space between the bearings carry BB load better than normal styles.