I am currently designing and building my own dual extruder FFF and have been looking at electronics.
For me the Megatronics V2 has the ability to do 3 extruders, but as you pointed out it only has 3 thermistor inputs (not a huge problem for me for my initial design but I want to eventually look at adding a 3rd extruder). I wonder if you can use the thermocouples at the same time as all the thermistor inputs? Has an SD card reader on board.
The RUMBA has screw terminals for most of the high powered stuff including the steppers which I like as it means less messing about with crimp connectors. It also seems to have enough inputs for all the thermistors you would need for a triple extruder machine. 5V is supplied via a switch-mode DC-DC converter it seems as well, so no hot 7805. SD Card is via an add-on.
Elefu needs to be soldered, although as I read it the SMT is presolderd so only through hole need soldering. Everything is screw terminal which should ease wiring. Uses a PC power supply which are easy to come by. Uses a custom version of Marlin though and SD cards are an add-on. Has something about lighting? This board is hard to find information about as there seems to be no documentation (on their website on RepRap Wiki) that I can find at the moment (even the size of the board, which seems huge in the photos).
Currently I am leaning towards the RUMBA, although I do like the Elefu RA board its lack of documentation makes it hard to decide as I can find out if it will do all I want (what are all the screw terminals for, how and what is connected to them). The Megatronics looks great but again only 3 thermistor inputs when it is capable or running 3 extruders and 1 heated bed is a flaw, sure it can use thermocouples but is that as-well-as or instead-of the thermistors? Not to mention I would rather just stick with one type of temperature sensor saves hassle debugging.