Was Robb's story irrelevant just because he was killed?
Robb didn't even had a single POV chapter. Daenerys had one third of a book devoted to her. Killing her without her making any kind of impact in the main storyline would mean that Martin has yet to grasp the very concept of editing, since Martin would have forced us then to read tons of filler content, Naruto style, while deliberately presenting it as a vital part of the story. Not to mention that Robb was able to severly affect the war in Westeros before his demise. As long as Daenerys plot proves to be vital to the Westeros conflict (either for good or bad, I don't care), I am fine with that.
But It has nothing to do with like or disliking Daenerys, and yes a lot to do with Lost -type of plot - building. Compelling stories rely on much more than "shocking" twists. Hell, even if destroying the reader's expectatives is a Martin's trademark, he can also play extremely well with the whole "and now happens what you are not expecting: the most predictable outcome" card (see also: Barristan the noble hero defeating the treacherous arena gladiator or Jon double - agent adventure with the wildlings yielding good results. What in other fantasy series would seem like a normal, cliched outcome, it is shocking for ASOIAF).