EU and MJ are mostly used for different purposes, and conversion methods tend to be inefficient or costly in some way or another. If you want to eventually use all the goodies in FTB, you're going to need to generate both at some point. It's not a one or the other kind of thing.
As for nuclear reactors, that depends greatly on the design you go with. You would do yourself a favor to go ahead and look up information about their mechanics, decide what sort of designs you'd be comfortable with using, and then decide if the output of those designs are worth it to you. At the very least, nuclear reactors tend to output a great deal of power over the lifetime of the uranium cells.
As for nuclear reactors, that depends greatly on the design you go with. You would do yourself a favor to go ahead and look up information about their mechanics, decide what sort of designs you'd be comfortable with using, and then decide if the output of those designs are worth it to you. At the very least, nuclear reactors tend to output a great deal of power over the lifetime of the uranium cells.