The control scheme is a result of RPG Maker, not the game itself. You're giving the game a strike for a shortcoming that it isn't even responsible for.
Blastoise, Vaporeon, and Glaceon have all been available for a while now. The other three will be available after the Elite Four, like many Legendaries in mainstream Pokémon games. This is nothing new. Finding Legendary Pokémon at this point in the game wouldn't make sense from a storyline or gameplay perspective, so they're rightfully unobtainable right now.
There will be content in the postgame where you can use your Articuno, Suicune, and Kyogre, but you won't be able to catch them during the main storyline.
The Pokémon aren't inaccessible because they're popular. They're inaccessible because they're so much better than every other Pokémon that people wouldn't even take others into consideration. When players use the exact same Pokémon in every single playthrough, then the game experience becomes repetitive and boring. This game is all about encouraging the player to adapt based on what is presented to them, making them think and strategize rather than just breeze through any obstacles with all of the best Pokémon. After all, a famous game designer once said, "Restrictions breed creativity."
This ideology appears to be at odds with your "I only want to use these six specific Pokémon" mantra, which I personally think is an extremely boring and close-minded way to play a game. I'm not saying that you shouldn't enjoy a game the way you want to, but I think it would behoove you to try enjoying a game in different ways, rather than just writing it off because you can't get a Kyogre. (Seriously? What sort of challenge would this game be if it let you use a goddamn Kyogre?)
TL;DR Don't quit the game for such an immature reason. Adapt, improve, and learn to experience a game in more than one way.
Timber Dragon and Bewilderer have both explained it perfectly. I strongly urge you to take their words to heart.