Now that I've finished building my Mk I fusion reactor (It awaits activation after enough fuel has been created - which will take awhile yet), here a few observations on the differences between ReactorCraft's fusion reactor and GregTech's, with the caveat that Reika's mods went through signficant updates since I played them last. Also note that it would be extremely hard, if at all possible, to build an ReC reactor in a limited-water setting without transfer nodes.
(1) ReC's reactor is more powerful by several orders of magnitude. Even GT's highest-yield recipe generates about 20 times less power than an ReC reactor. In addition, that generation is completely self-sustainable and requires no non-renewable resources, which GT's only does with its lowest-yield recipe.
(2) As opposed to GT's reactor, ReC's reactor can't use different recipes (that may have changed, I recall it was in the plans) and consequently it is not variable in its output - though that does not matter much since keeping it running costs no non-renewable resources. It also can't make rare elements through fusion.
(3) You can actually shut off GT's reactor. Long-term operation is desirable, but you can shut it off completely without your base turning into lava (I'd like to know if Reika has addressed this since).
(4) GT's reactor requires many more different materials, and many more rare materials, to construct than ReC's, while ReC's requires significantly more material in total, but almost all of it is reasonably common. In addition, RotaryCraft - through which you must progress if you want to build the ReC reactor - provides efficient means to gather those resources, while GT provides no help at all.
(5) The materials for both reactors and their supporting infrastructures require significant amounts of secondary processing, but GT's take drastically more time - I count ReC in real-time hours, GT in real-time days. This is also because RotaryCraft provides more efficient power generation at lower levels, so that you can power your processing machines efficiently, while with GT, the power required to run parallel processing on the same level would require exactly the fusion reactor you are building.
(5) Crafting of reactor components in GT is significantly more complex than in ReC, but GT machines are, as a rule, much easier to automate than RoC/ReC machines. AE2 integration comes naturally with GT (in fact, I don't think I know another tech mod except EnderIO that makes it so easy), with RoC/ReC it's a PITA.
(6) The supporting infrastructure of an ReC reactor requires more different machines and processes, GT's requires more "machine spam".
(7) ReC's reactor takes up significantly more space, which makes it much more difficult to integrate it into your bases.
(8) To generate power with GT's fusion reactor, no magically overpowered farming is required.
(9) ReC's reactor looks cool in operation, GT's is unimpressive since you don't see anything happening.
(10) ReC's reactor is more realistic in several ways - two examples: it should not be possible to extract tritium from deuterium in usable amounts without exposure to radiation, and it should not be possible to store plasma. Thus, some method of getting the power out of the plasma should be an intrinsic part of the reactor structure rather than a separate machine.
All in all, I don't think I can rate one as preferable over the other. Both have their strengths and their weaknesses, which balance out if you take into account both building and using them. With one exception: I really wish I had my teleporting mining frame carrying four RoC boring machines from my FTB Monster world. Resource gathering in GT....may just be the post painful thing I've ever forced myself to do in modded Minecraft.