On to the questions of the OP, then:
What surprised you as you played through the game?
Oh, a lot of stuff. The first time I got an alternate camera angle when healing in the Poké Center. The sheer amount of available Pokémon. How nice my house looked. Interactability with the Rhyhorn in the garden. All the numerous little details, the objects, textures, many of them used just in one or two places to create atmosphere specifically for that place. For instance, the aquariums and statues in Ambrette Town Aquarium.
Not to mention, the enormous size of the Kalos region. Specifically, how big Lumiose City is. Heck, I bet it has more content than most cities put together in any other game in the series. It took me hours to explore it. The Art museum was also a nice touch, I was surprised to see some of the pictures in there were taken from the TCG.
This game was literally full of surprises, and surprisingly many mysteries too. The ghost girl in Lumiose stood out as the most intense one. But I also had a laugh at times, such as when the fairy type was introduced, with the reaction of the other NPC interrupting the introduction with "It totally changes everything!", possibly a nod to the reaction of fans of the series. Another fun moment was the story of the castle in Camphrier town. It was built up to be a long, epic tale with a mystery or something thrown in, but it turned out to be as eventless as a castle's history can conceivably be. Hilarious. I was also honestly surprised to finally see a toilet in the Pokémon world (located in Laverre Gym).
What disappointed you as you played through the game?
Not a lot, but I'm afraid a few things stood out. First and foremost, the rivers. The Kalos region is crisscrossed with rivers, but none of them are traverseable. One of the rivers goes straight through Lumiose City, continuing past the power plants in the desert before ending in Azure Bay. Following it upstream from Lumiose would take you through Victory Road before the river froze over close to Snowbelle City. Another river goes from Vaniville Town, through Aquacorde Town, passing Camphrier Town and Route 7, and ending in Cyllage City. These rivers would have made perfect late-game shortcuts and/or sightseeing routes, but were totally ignored.
Coumarine City was also bit of a disappointment. Great idea with the monorail splitting the city, but I was disappointed that they didn't show anything of the view from the monoral as you took it up/down the mountain.
I had also looked forward to see where the railroad tracks went from Couriway town, as they had stood out as truly mysterious on the Kalos map artwork released in May. "Nowhere" turned out to be the answer, at least for now. Another teasing terrain feature, the race track in Cyllage City, which I had anticipated to host a bike race at some point, also remained unaddressed.
Also, there are too many settlements in Kalos starting with the letter C. I have a hard time telling Coumarine and Couriway apart, and Cyllage and Camphrier are not making it easier to remember the names of the various cities.
Last, overworld weather is nice, but... why do we still not have any routes with sunshine? I mean, that one, non-repeatable time in Ruby and Emerald didn't fully satisfy my want for sunshine (hey, I'm a Norwegian, OK), and strong sunlight is at least as common as rain, on a global scale. I don't see why the deserts always have to be sandstormy, wouldn't intense sunlight also be just as fitting? With fog, hail and sandstorm being so common, one would think GameFreak would have made another sunny place by now.
How could they have improved the game to remove this disappointment?
Simply put, they could address them in the future. G/S/C was also full of places that kept teasing you with more than they ever delivered (stupid Underground Path and the hint at trainers battling there). I hope X/Y won't go down the same route. I hope the rivers will become traverseable in the inevitable third installment, looking at the Kalos map art they seem too promising not to (not to mention that many of them converge towards a cloud-shrouded area in the very south). I have high hopes for the future of Generation Six.
What parts of the game do you enjoy?
All of them, pretty much. Battle Chateau is really nice. Just swishing around Lumiose City, trying to learn its layout and the locations of its various features. Shopping, and seeing that large sums of money is addressed properly in this game. Finally, there are game elements requiring you to shell out a bit, digging into your wallet instead of you having virtually endless money about halfway through the game. Having hundreds of thousands of Poké Dollars isn't mundane wealth anymore, it simply enables you to pay for the most expensive wares and services. A restaurant meal costing several tens of thousands simply seems natural.
I also enjoy the good ol'-fashioned Pokémon training. Acquire 'mon, train 'mon, kick ass with 'mon. As fun as it has always been, perhaps even more so since continuously expanding movepools allow for a lot more diversity in strategies when using the same Pokémon as you have before. Beedrill is a prime example of this.
Which Pokémon did you really enjoy using?
Beedrill, as per above. Having endured its hilariously shallow movepools in the first three generations, it was nice to finally see it learn decent attacks after six generations of existence. I also acquired a Rotom-W, which performed surprisingly well, and never let me down (apart from when Hydro Pump missed twice in a row against the Champion's Gardevoir). Honedge/Doublade is also a brilliant 'mon to use, always having the moves for any situation, it feels like. Aerial Ace, Shadow Sneak, Iron Head, Sacred Sword... whenever I needed something to take a hit and strike hard in return, Doublade never let me down. A shame it plays a lot differently as Aegislash, getting somewat of a 3MSS, since it's almost "forced" to run King's Shield.
Which Pokémon ended up being a lot worse than you thought they would be?
Venusaur. I guess I didn't use him right; with a movepool consisting of Strength and tons of Grass moves, his use was only situational. Okay, Razor Leaf (and later Petal Blizzard) hit opposing Hordes, and Sleep Powder put things to sleep, but I felt he only shined against foes weak to Grass. I guess I should have invested more TMs on him, and settled for one stat to play on. Petal Dance is Special, Petal Blizzard is physical, giving both of them pretty big downsides when his best offensive stat is Sp.Atk. He got a little better once Sludge Bomb was available, so I guess Venoshock would have helped too, if I had thought of using it. Oh well, there are always reruns.
Which gyms did you find the most challenging?
Honestly, none of them. Even being only slightly overlevelled (often only by a level or two), none of the gyms felt any threatening ever. I attribute this mostly to my experience, though. Knowing what type of Pokémon a gym leader uses, I open the fight with the Pokémon and the moves best suited to take them on. A Fire type against the Bug gym, Ghost types against Fight, Water against Rock and so on. The Pokémon games become a lot easier when you know what you're doing. Not to sound arrogant or anything, it's just that I feel that I know too much about the games and strenghts and weaknesses of its Pokémon for it to be difficult. I guess first-time Pokémon players will find the gyms, and later the Elite Four, a lot more challenging than I would, knowing what I've learned over the years. The level of challenge I find the most fun (I played a hack game once where I really had to fight hard for every badge, often taking many tries before I won) would just be frustratingly hard for less experienced players. GameFreak have to design the game so anybody can enjoy it, which means setting the difficulty at a reasonable level. If the "hardcore crowd" want challenges, they can always fight each other.
P.S.: What the heck does tipping do? This has troubled me ever since launch. I love a good mystery, but one would think the extremely resourceful Pokémon community would have landed on a definite conclusion by now. It's been four weeks.