Typhlosion
Ability: Blaze
Nature: Modest/Timid
Moveset:
Eruption - Great when HP is full, STAB
Lava Plume - Good chance to burn the target, STAB
Flamethrower/Fire Blast/Blast Burn - Flamethrower hits more often, while Fire Blast will do more damage if it hits. Blast Burn does the most damage overall, but you have to rest the next turn. If you're going the safe route, I suggest flamethrower.
Solar Beam/Focus Blast - Both are for coverage, but Solar Beam takes time to charge and Focus Blast barely hits. I recommend Solar Beam, but Focus Blast works too.
I chose Typhosion because he is arguably the best starter of the three. Feraligatr is good as well, but since there are so many other options for water types, I chose Typhlosion. As for Meganium, she didn't exactly work out for me the last time I used her. Typhlosion has an advantage against a fair share of the 16 gyms, and with it's beautiful speed and special attack, it makes for a great speedy sweeper.
Crobat
Nature: Jolly/Adamant
Ability: Inner Focus
Moveset:
U-Turn - Used to deal damage and get crobat out of sticky situations. Thanks to Crobat's high speed, this can be done quickly and easily.
Fly - Useful in-game because you can fly to any familiar town, STAB
Cross Poison/Sludge Bomb - Crobat's best Poison STAB
Mean Look - Used for catching the wandering legendaries
Crobat's amazing speed and decent attack stats make it one of the best choices for a flying type there is. It helps with a good amount of the gyms, and Mean Look helps with catching the wandering legendaries A LOT. Crobat is also available very early on, right before the first gym.
Quagsire
Ability: Water Absorb
Nature: Brave/Naughty
Moveset:
Earthquake - Powerful, STAB
Strength - Needed for in-game purposes
Surf - Necessary to beat the game, STAB
Waterfall - STAB, best physical water type move that quagsire has access to
Quagsire might not be the best choice for a water type, but with one weakness and two immunities + the access to all of the HMs it can learn makes it a huge help in-game. Not only that, but it has immunities to three of Red's Pokemon, proving useful in the final battle.
Ampharos
Ability: Static
Nature: Modest/Rash/Mild
Moveset:
Discharge - 30% Paralysis, STAB
Thunder - Powerful, STAB
Signal Beam - Used to deal with Psychic, Grass, and Dark Types
Power Gem - Coverage
I honestly love Ampharos. It's available so early on, evolves at an early level, and has impressive stats both offensively and defensively. It also has a wide movepool which helps in all sorts of ways.
Espeon
Ability: Synchronize
Nature: Modest/Mild
Moveset:
Psychic - Powerful, STAB
Shadow Ball - Coverage
Signal Beam - Coverage against dark types
Future Sight - Powerful, STAB
To be honest, espeon is my favorite eeveelution. She has a huge special attack stat and impressive speed, making her one of the best psychic types available in the game. She is also available early on (around the fourth gym)and has an advantage over lots of the gyms.
Dragonite
Ability: Inner Focus
Nature: Adamant/Lonely
Moveset
Fire Punch - Coverage
Outrage - Powerful, STAB, you don't really have to worry about confusion in-game considering that you can switch out after a KO
Dragon Rush/Dragon Claw - If you want to hit more often, go with Dragon Claw. If you don't care about accuracy and just want raw power, go for dragon rush. With the wide lens dragon rush's accuracy is more reliable
Aqua Tail - Coverage
Although only available late in the game and evolving late, Dragonite's balanced stats and crazy attack come in handy in the second part of the game.