On Eden:
I think the relationship with Gaia and Ryne is a bit forced in terms of how fast it's developing, but then again these aren't "typical" people in any sense of the word. Is it really fair to to Ryne to speak of how young she is when she's the heritor of at least a hundred+ years of memories and feelings? For all we know, Gaia may have a similar situation she's coming from. The ease with which they establish their relationship might be due to something deeper. Maybe they've done this before, on some level or another, thousands of years ago. If, as many people suspect, Ryne is the soul of Venat, then logic would dictate Gaia is the soul of the original Elidibus. I suspect there's a deeper connection than simply a spot of tea over coffee biscuits.
As far as Ryne's idea to be the vessel for Shiva, I took it as she was hoping to contain the power in a more stable, safer form, mistakenly believing that her affinity for Light would give her an advantage over Ice. Ultimately, her goal was to both build her own aether-controlling muscles and to try and ease our burden as we bring the element of ice back into the world. Of course that didn't happen, but we ended up with an awesome fight and some character growth in exchange so I'm fine with it.
On ice making plants grow:
Now, as to why the ice element would make plants grow, I can only think that - in general terms - ice is gentler form of the stasis/order that light brings, acting as a kind of aetherial "glue" that binds the myriad elements together. Probably exists in trace amounts everywhere, even if "ice" itself isn't present for anyone to see.
MSQ:
My take on Elidibus and his actions is that by awakening so many people to the Echo, he further divides Hydaelyn's powers, weakening her just that much more. Then there's the obvious setup of people with good intentions being misled by a bad actor to work against the good guys for all the wrong reasons.
I'm also curious about how G'raha is going to get through all of this, or if he'll end up giving all his life to ensure the Scions make it back to the Source.
Qitari:
Maybe it's just me but I see the restoration of the stelae from a purely gameplay perspective. SE wanted us to be able to choose what the history of the First (specifically the Ronkan Empire) was going to be remembered as. I chose the optimistic route for the first option, as based on what I know of the Ronkan Empire, it's rulers tended towards a wise, careful approach, and it seemed more likely that they would look upon the Qitari with curiosity instead of attempting to subjugate them. The presence of four distinct races as the foundation of the empire (Ronsa, Drahn, Qitari and Viis) hints that subjugation was unlikely, and that the Ronso who led the empire likely saw the merit in bringing each race into the fold to create a greater whole.
For the second stelae, I looked at how the Viis acted when we first met them and simply applied it to the Qitari. Here we have the Viis migrating as a people to Rak'Tika, coming across a new race they had nver seen before, out of their element and unsure of the dangers presented by this massive forest they now find themselves in. Reacting with initial hostility fits with the character of the Viis, but as aggressive as they can be, they are not without reason. So what started as a bit of a diplomatic faux pas with the Qitari was resolved rather quickly, and the Viis - clearly a proud, skilled people - were again brought into the fold, likely with the Viis swearing their allegiance to the empire in part as recompense for how they felt they mistreated the Qitari upon first meeting them.
Of course, that's just my interpretation. Part of the fun is we get to build that world for ourselves. But that's all I think it is; a gameplay element that let's us build some world history. Plus we're the Ally of Ronka, which apparently means we're basically infallible.