The issues with the plotting of Daenerys' storyline is less relating to the logistics of it so much as it is the practicality of events. Daenerys, unlike the other majority of other characters, has little effect on any of the other primary characters right now, nor has she since the first season, where we had three extremely prominent, different characters in the form of her, Viserys, and Khal Drogo in her proximity, all with different dynamics to one another. Since then, we've had a rather one-note story, which is completely in line with her character but isn't, to me, rather compelling, and makes it feel static. Those she interacts with have similar power dynamics and interactions towards her (Daario, Selmy, Jorah, Grey Worm) even if there are some differentiating features, and there isn't enough time available to flesh out the story more thoroughly and explore different facets of her role as leader. Given her limited interaction with a wide range of other well-developed, different characters she's left to stand on the strengths of her character but she doesn't have the complexity, nor the time, to be particularly compelling alone.
If we take others such as Cersei for example, regardless of whether you are somebody who enjoys or dislikes the character, the variety of her interactions with others are quite dynamic, from her and Ned Stark, her and Jamie, her and Joffrey, and her and Robert in season one, to the current interactions with her family and the Tyrells, it's interesting to see how the character reacts to the constantly shifting power dynamics brought about by changes within the world, and this helps to develop her character further as we see these interactions. Daenerys is really missing such a variety of encounters, season one a notable exception where she had a compelling arc with Drogo and grew notably as a character. Since then she has been developing but it's all been in the same direction on the same points (and this is why I firmly believe she's going to end up with immoral eventually, given how much they're pushing her in this direction), with similar obstacles opposing her, interacting with characters who have similar viewpoints and rarely interact with each other, without having much impact on the primary cast (perhaps this is changing given how it's affected Tyrion in relation to Oberyn but I must confess it doesn't seem so unless Daenerys will head to Westeros after Meereen). Her story has more than enough material to make it compelling, but it feels like a spin-off inside the main show at the moment, and this is holding it back as it doesn't have enough time to delve into deeper topicoks to make it more engaging, for myself at least.
In short, the complaints relating to Daenerys is that her arc feels rather static, one-note, inconsequential (in the journey, I think everybody's in agreement that she will be a major player at some point in the future), and repetitive in nature, not that the actions she's doing are unnecessary, illogical or nonsensical. Perhaps others see it differently (and I know I've commented very similarly awhile back, but I just hope this better clarifies what may be the reason for such complaints, even if you disagree).
EDIT: Also, Jamie raping Cersei at their dead son's wake (or that's what it seemed to be, not sure what the ceremony is called in Westeros) was not something I expected given how Jamie's arc had been going. I'm curious about the motivation. Love mixed with hostility for her suggestion to kill Tyrion? Love mixed with hostility over her unwillingness to sleep with him prior to then? Or is it another aspect I'm ignoring? I'm not really clear why he did that. I can understand why he'd want to continue sleeping with her, having been returned to the family, and his love, after an ordeal, but this, in that location, had me stumped honestly.
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