At first I thought the blue laser doubled was going to be the best, but whilst they cut through many enemies like butter, by stage 23 or so it was hard going. I can't be sure it's any better than the standard weapons on the 5th tier ships (Kongregate confirms this- the Pseudo-Epic ship outdoes the blue lasers quite easily). However I didn't realise that you could make certain combinations, so I'll test them right away!
My test right now is the final Nekon attack, the 620 black orbs in 60 seconds, since this is the only thing I haven't finished in the game (aside from a few achievements).
I've confirmed that the blue laser doubled up is nowhere near as good as fusion synth. I guarantee you won't be able to finish platinum nekon attack with the blue lasers, regardless of how many buffs and auxillary weapons you use. But it was a cinch with the fusion synth.
(Note that fusion plasma, while more powerful, isn't as good for Nekon attack as it's a weapon best aimed and with a low fire rate, compared to the fusion synth which shoots spread beams.)
Strop, while I did some other research, and cannot debate that blue laser is worse than fusion synth, I can tell you that you're wrong on one point: I did the Black Orb Platinum nekon with single blue lasers.
It was really hard, but I did it. Hint: High-level mega-blast, infinite bosskiller missiles (from upgrade in Black Market), Relentless Strike, Bonus Magnet, and warpspeed. I just turned on my missiles, held my mouse down (angling across the screen) and spammed my mega-blast, relentless strike, and magnet, using warp every time I slowed down. I finished with a few seconds to spare, too.
Best way to finish nekon attacks is warpspeed and time stop combo. You use warpspeed till the screen is filled with nekon ships and hit then the time stop skill. This skill stops not only other ships, but also the mission time counter. You have plenty of time to kill all the ships and collect the orbs. Shortly before the time is normal again, hit the warp again to start with maximum speed. Rince and repeat and you finish all nekon attacks with plenty of time to spare