Sounds like FFXIII and few would say it has a great plot lol

Two are not worth comparing.  Xenoblade is comprehensible with believable, developing characters.  And the gnosticism serves as an underlying theme, not something necessary to grasping the themes of the story.  Xenoblade Chronicles is well executed, Final Fantasy XIII is horribly executed.  If you don't like the story, that's your own business.  I don't like The Great Gatsby; I don't care for Hamlet.  I still recognize their artistic achievements and qualities. 

Implementation is FFXIII's problem. 

Guys, I have a question: Can I save side quests to later?

I mean, I have found some side quests, but I want to continue the story. Are there any side quests that expire?

Yes, they are labeled. Anything with a little clock (I think that is how it is shown?) next to it expires after certain story events. Everything else is okay to leave for later. 

I can't remember if any expire exactly, but there is an area that will be removed from the map around 2/3 way into the game (I think). I think some sidequests require item collection or monster hunting from that area...but I'm pretty sure there are other methods to get around that. Can't remember exactly....I think I just resigned myself to focusing on the more plot-focused sidequests over the hunting/collection ones. I'd recommend looking at a guide when you get to Sword Valley, if you're really worried about it.

It takes more than a comprehensible plot for a story to be great. Mario games have a very comprehensible plot but not necessarily a great story (though that's because they aren't really trying to tell a story). Xenoblade's plot is well executed enough because it doesn't try to tell a complex story. That still doesn't make the story great. On the other hand FFXIII did try to shake the formula and took a lot of risks doing so but obviously failed at it. Still had FFXIII's plot been more comprehensible it would have made for a great storyline because all the ingredients were there, simply not in order. But Xenoblade's plot felt very familiar although indeed well told. Sure that might just be my opinion but I too can objectively recognize strengths and qualities.

I thought the story was above-average as far as complexity goes. Like I said before, the story has many literary devices riddled in it. 

Well familiarity doesn't necessarily make a game less of a great story.  Many of the stories perceived as "great" are not new at all, they just did it better (see Shakespeare).Familiarity crosses the line into the territory of being an actual flaw when the implementation of convention becomes cliche.  I would say Xenoblade doesn't cross that line. 

  And I would say the story of Xenoblade has its complexities and depths, but they are layered in such a way that one layer can be grasped without the other (for example, the whole of the story is an allegory of the Gnostic mythology from beginning to the end, but you don't *need* to know taht to appreciate it).  In that way, I would actually compare it to Shakespeare actually, whose works had layered meaning, but the universals could be grasped by essentially everyone without digging into the depths that reqired more knowledge to understand.   Xenoblade is the same, as the story gains a new level of interest and meaning when you are aware of the basics of the Gnostic mythology (similar to how knowing period Christian beliefs and classical literature helps you with Shakespeare).

The plot of FFX was absolutely batshit crazy!!

The storytelling and character development was brilliant though. I think it's important to separate those.