Perhaps it's the Metroid fan in me, but I enjoyed the less linear approach to the story...almost like it wasn't forced on the player at all...especially since at times you were required to complete certain sidequests before progressing forward...I very much enjoyed exploring the areas, sometimes just wandering around for hours after discovering a new region...and I just planted the probes as I went, which gets easier once you get your Flight module...
I've only barely dabbled in Xenoblade 3D so far...I'm pretty much still in the beginning so I still can't really explain how things were handled differently, save for all the tutorials at the beginning telling you how to play...but I managed to figure that out pretty quicly in X anyways (and it reeeeeeally helps to read the Manual as well)
The only thing that really bothered me about the Final Boss was how it jsut plain forced you to fight on foot, by drainging your fuel...It all comes down to your preparation really...Were your Skells at their highest levels? Did they have strong weaponry? Did you equip good Augments? Are your levels up to snuff? Is your squad's level up to snuff?
Did Celica still not figure out what the power-up button was? If your having troubles then you might want to do a bit of grinding and you might need to do a bit of money spending...
Might I ask what levels your characters are at
Cutie Gwen
?