Firstly, I would like to say that players are having trouble playing our game since they are unable to find the location of the Battle Tower, the Safari Zone, the Sky Pillar to catch Rayquaza, the way to travel to Hoenn, how to get all the different types of Hidden PokeBalls and Reusable TMs, and how to access the 4 different catching zones to catch Pokemons.
So below your starting point in the Diabari Route, if you go south through the bridge at the right of the pond, you will be able to access the Diabari Field which is located at the center of the 3 catching Zones. In the Diabari Field, there will be a teacher next to Professor Joseph who will give you a lv48 Mareep that will evolve into an Ampharos by lv50 which is one of your starters alongside the lv50 Eevee and Alakazam you get by 2 different people after you get down from the bus at the beginning of the game. On the east, west, and southern part of the Diabari Field, you can access the 3 different catching zones(the Water, Fire and Grass Zones respectively) where you can catch a variety of wild pokemon, and make up your team as per your wish. There is also a 4th catching zone in the school hall between the entrances of the infirmity and the School Tournament, where you can get a variety of Normal, Flying and Water Type Pokemons. (Even Rare Pokemons such as Feebas can be found easily in the Water Zone and their respective zones.)
The secret passage area in the garage which is on the right of the Second Entrance to the school hall.
In addition to the School Tournament, you can also access the Battle Tower to battle with your Pokemons there since the starters you get are all lv50(you can use the 2 rare candies your starters are holding to level up your lv48 Mareep to an lv50 Ampharos or you could train it up on the catching Zones and use the Rare Candies on some other Pokemon) Even the Pokemons in the 4 catching areas are from lv40 to lv48, so you can easily train them up to lv50 to challenge the Battle Tower with a team of your choice.
The Battle Tower can be accessed if you enter the garage(the rightmost third set of entrances to the school) After entering the Garage, you will see four different staircases leading you to different places on the North end of the garage. One of them will take you to the Battle Tower where you can do as many battles as you like.
To access the Safari zone, you have to enter the garage. On the north side, one of the 4 staircases will take you to the Safari Zone, which is the 5th but not the last catching zone, where you can catch even more varieties of rare Pokemons as per your choice and build your team with more Pokemons.
To catch Rayquaza in The Sky Pillar, you will have to go to the garage, and one of the staircases will lead you to the Sky Pillar.
To catch Rayquaza, you will need a Mach Bike which will be given to you by a guy with yellowish hair in The PokeMart
To catch Rayquaza and the different Pokemons in the 5 Zones and in Hoenn, you will need PokeBalls, Great Balls, Ultra Balls, and Premier Balls, which are hidden in the bushes and rocks of the 3 different catching zones, and can also be purchased in the PokeMart.
The Reusable TMs can be also be found hidden in the different rocks and bushes in the 3 different catching zones, which are useful TMs and can also help you in catching Rayquaza.
The different evolution stones can be also be found hidden in the different rocks and bushes in the 3 different catching zones, which can be used to evolve your Eevee and other Pokemons.
To go to Hoenn, you will have to go to the garage, and if you enter the staircases that will be leading you to the Sky Pillar or the Battle Tower, you will also an NPC at the south of the area, who will take you to Lilycove City in Hoenn.
Actually, you get an lv50 Alakazam from the kid you meet after you get down from the bus. And the man on the right of the kid will give you an lv50 Eevee, and below the Diabari Route, on the Diabari Field the teacher on the right of Professor Joseph will give you an lv48 Mareep which will soon be an lv50 Ampharos by leveling up or using the 2 Rare Candies, the starters are holding. You can also catch other different Pokemons in the 4 different catching zones (3 of them around the Diabari Field and one of them inside the school campus) using the hidden PokeBalls in the bushes and rocks. You can also catch some Pokemons in the Safari Zone, and since all Pokemons are from lv 40 to lv50, you can train and use the lv50 Pokemons in the Battle Tower and also in the Battle Tournament in the School where your Pokemons do not have to be lv50. You can also use the hidden TMs and evolutionary stones to strengthen up your team and catch Rayquaza in the Sky Pillar. You can then also go to the Hoenn region.
The portals to the Battle Tower, Safari Zone, Sky Pillar to catch Rayquaza and to Hoenn is through the 3 different stairways inside the garage of the School which is the rightmost entrance to the school.