I think most of the significant issues have been brought up here (the colors, a few games crashing on the 4.1 firmware, SRAM save issues with the jailbreak firmware). The most recent firmware fixed the colors and most of the crashes. Monopoly is still a threat, apparently, but kevtris has said he has a fix for that on the way. There have been a few other miscellaneous graphical glitches mentioned; it's not always clear whether they are Super Nt issues, SD2SNES issues, dirty cartridges, or what, but they're being looked into. Obviously cgatto's hardware failure is an issue but that seems to be an isolated occurrence. Most people seem pretty happy with it.
One minor thing I haven't seen mentioned here is that the "menu bounce" option disappeared in the 4.3 firmware; that is also being fixed.