Skyrim. I'm generally a bigger fan of JRPGs over WRPGs but to me, Xenoblade is a JRPG trying to be a WRPG and I frankly just think the genuine thing is better in nearly every respect.
Combat: I don't understand the gushing over the combat systems of either game. Skyrim's combat, though improved over Oblivion's, still largely just consist of kiting the enemies and Xenoblade's combat isn't much better as it too revolves around a singular strategy; Break > Topple > Daze (And for both games, once you inevitably get to the point in which you're over-leveled, you can trow all strategy out the door and proceed to curb stomp everything with little effort). Can you do things besides the aforementioned? Yes. Is there any beneficial gameplay reason to do so besides roleplaying? No. With games like Dark Souls and Witcher 2 having also come out this year, it's almost insulting hearing about how "great" Skyrim's and Xenoblade's combat systems are.
Art Design/Direction: Xenoblade is more fantastical and Skyrim is more realistic. Both are done very well and it's a complete matter of personal preference as to which is better in this category (I like both).
Exploration: It's this category specifically that I think Bethesda's years of experience making open world games puts Skyrim leaps and bounds over Xenoblade. One of the biggest complaints against Oblivion was that, even though the world was large, it was mostly filled with empty space and repetitive dungeons. Skyrim hasn't completely rectified this problem but has done a significantly better job than Oblivion in providing a wider array of landmarks (by this, I'm referring to Forsworn/Bandit/Giant camps, towers/forts, ruins, small towns, shipwrecks, ect.) and dungeon types to discover and explore. Xenoblade has significantly fewer dungeons so there is no fear of repetition there but it's overworld maps on the other hand, are largely just wide open spaces. Landmarks are generally just some form of geography (lakes, waterfalls, mountain/hill) and the secret locations were mostly unimpressive (they were mostly just geographical landmarks {usually a small alcove} where you would find sidequest items or unique mobs). Xenoblade's greatest crime in this category though is very, very few treasures/loot to find. Maybe this is just a product of being a long-time gamer but if I'm taking the time to go off the beaten path, I expect to find a treasure chest filled with phat loot.
World Building: Really don't think there is much of an argument here. Whether you like the world of the Elder Scrolls games or not, I don't think it can be argued that the world's lore is very extensive and detailed. Between all the books, NPC journals/diaries, and set pieces, I think this category also handily goes to Skyrim. That said, Xenoblade does do a good job giving their cities some life by having NPCs on schedules and having different groups of NPCs on the day and night cycles.
Story: Both are pretty par for the course. Skyrim's main story is probably the least interesting story told in the game (compared to sidequest and creating your own stories) and Xenoblade is typical JRPG fare in that the story starts out relatively normal and interesting but gets progressively convoluted and up it's own ass as you near the end of the game (It's not as bad as Xenosaga though). I'll just say that I think the main story in Xenoblade is more interesting than Skyrim's but the number of interesting stories in Skyrim outnumbers Xenoblade's (like 95% of the sidequest dialog in Xenoblade is completely forgettable/irrelevant).
Also, I don't think either game is particularly unique, or rather, they are only unique within a certain context. Bethesda games as a whole are relatively unique as there are very few developers even attempting to make an RPG with similar design and scope. That said, Skyrim is just another Bethesda game and beyond benefiting from the natural progression of Betheda getting better at making that style of game, isn't doing too many new things. Same goes for Xenoblade. When compared to other JRPGs, Xenoblade and FFXII exist in their own little privet bubble which spawn all the comments about Xenoblade being a unique game but everything in the game has been done elsewhere, mostly borrowed from what's generally associated as WRPG or MMO game design. If you play a variety of RPGs, it's highly unlikely you'll run across anything in Xenoblade you haven't already seen before.
That all said, you shouldn't ignore Witcher 2 or Dark Souls either. W2 for a good story-driven experience and Dark Souls for a combat/skill-driven experience.
