Step 1

Choose a good starter. Charmander, Eevee and Squirtle are always good, strong starters. Choose a good secondary starter. This will be the main starter's partner and is computer controlled. It is a good idea to choose a type that is stronger than you Pokemon type. Take note that you cannot have two of the same elemental types. For example, no Totodile and Mudkip.

Step 2

Make sure you do lots of missions. The training Dojo, with the exception of the trohpie and dragon lair is a complete waste of time. You always want to do B rank missions and up. Always store up a lot of items after each trip and save money, you will need these later. Big/Huge Apples, Reviver Seeds, Oran Berries, Max Elixers and Gravel Rocks are essential.

Step 3

Teach your Pokemon moves that can beat at least one type stronger than it, defensive moves like Thunderwave or Protect, and Stab moves for extra power. This may sound insane, but you want to get to at least level 22 before you and your partner go on the run. This will take lots of time to do, so do not rush. But if you take the time, your Pokemon will beat most any Pokemon on the way.

Step 4

When you reach Thunder Wave Cave, that would be the time to level up early in the game. Do multi missions {a bunch of missions in the same dungeon} until you get to level 15. Continue the multi missions until you get to Thunder Mountain, Or Zapdos Mountain, whatever. You Pokemon will be over kill. I recommend training at Zapdos Mountain before you get to the Great Canyon, as this will set off an event.

Step 5

Learn that while on the run, you wil notice two mini dungeons that you can only do at that point in the game. you can do these lover and over. Do not take items, as you might faint and waste them. By the time you get to magma Cavren, your Pokemon should be no weaker than level 30. This dungeon is easy, but make sure to stack up on pecha scarfs, huge apples, pecha berries and/or heal seeds.All of this extra prep is not for the dungeons that your going to, its for the Sky Tower, the worst dungeon in the main game. Ghost Pokemon, arodactlye (sorry about spelling) , nine floors after the save point and very few items, this dungeon will frustrate you. Luck plays an important role, You also want about 7 max elixirs so that you and your partner/s can use powerful moves as many times as needed. When you get here your level should be level 35+ so that you can beat all the other Pokemon easy.

Tips

Always have money in the bank. The bank is run by the Persian.
Link moves are a huge help in boss battles, but the make your belly go faster.
Thunderbolt and heatwave are very useful in a Monster House.
If you've played a Rogue or Roguelike before, you should have no problem with this game.

Warnings

Never steal from the Kecleon shop that are sometimes found in dungeons. They will kill you quick. They are at LV 90, actually. They can take 2 turns at once. However, they have quite low health, so a LV 100 can defeat them easily if not ganged up on. Stealing is the only way to recruit a Kecleon on your team. You must have a Friend Bow, and they will be recruited 0.1% (1/1000) of the time.