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I have the game too, and it is great. You're up to Sky Tower, too? Do you know how to attack those Shuppets that stay in the walls? I can't get past the first level of the Sky Tower because the Shuppets keep attacking me from inside the walls and I don't know how to fight back. So I've been doing other missions to level up, get more items, and add more pokemon to my Friend Areas while I try to figure out how to attack through walls.

As for what pokemon I started as, when I took teh test it said I was a Totodile. I didn't want to be a Totodile, so I restared the game. When I took the test again it said I was a Chikorita, and I didn't mind that. My parter is a Charmander, because it's one of my favorite pokemon.

They're quite good, in my opinion. If you want to see some, Serebii.net has quite a few screenshots: www.serebii.net/mysteriousdungeon/

Yay, I managed to beat Rayquaza! Theres an odd story to go with that, though.
The first time I tried that dungeon, I went in with a bunch of items, ready for a long dungeon. I was beaten on the first floor by a Shuppet. I didnt want to lose all my items, so I turned of the game without saving again tried again. The exact same thing happened. So I came to this board for suggestions, then leveled up for a while as I figured out what to do.
So today I decide that if Ill end up trying the dungeon and keep getting knocked out until I manage to get to the end, I dont want to see that long story cutscene every time. So I decide to go in the dungeon with no items, not even holding anything, so that when I die the first time I wont lose anything.
I try it, and manage to befriend a Shuppet on the first floor, which helped. I decide to keep going as long as I can before getting knocked out. I manage to get through the entire thing, living off the items I picked up in the dungeon. Unfortunately, the Shuppet was knocked out on floor 25, the floor before the Kangaskhan statue that you can save at. So the party is just me, my partner, and the Wooper I brought along when we get to Rayquaza. I throw a few Silver Needles at Rayquaza, then when he was right in front of me I used Body Slam and Razor Leaf a couple times (and my teammates attacked him a couple times when he moved up). And that was all it took to beat him.
Im still marveling at the fact that I managed to get through the entire dungeon with no items on me. Though Im sure being level 40 helped. (Wooper was, I think, 25.)

And the ending of the story is really sweet. ^_^

Just before you reach a Tropius, you could try setting Mudkip's tactics to "go after foes," set the IQ to "Exclusive move user" and only have Ice beam set. Then walk toward/up to a Tropius and walk away from it one square (step toward Mudkip). Mudkip will switch places with you, and as long as it sees the Tropius it'll go attack it. Just make sure to save some Ice beams for Rayquaza, those will come in handy.

I was going to teach Ice Beam to my Wooper, but I hadn't yet taught it to him when I went into the tower.