Nothing wrong with the Gen2 electronics :-). Still driving my 'bot after a year or so.
If you want a more recent extruder design, you will probably need another stepper and stepper driver board. You'll also need a controller - the gen2 could *just* about squeeze onto a basic arduino, but the firmware has outgrown it a little while ago. I'd suggest getting an arduino mega, and wiring the gen2 'tronics to a shield. The mendel should be capable of being driven no problem.
Nothing wrong with the 1.1 - just that they used to get a bit hot (grab a bigger heatsink) and are through hole soldering - SMD is actually quite a lot easier and better suited for mass-production, like the makerbot.
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