Route & Choices

Monster Girl Quest! Paradox RPG counts several moments where Luka is forced to make important choices between two options available. As each option locks content for the current playthrough, the pros and cons must be weighed each time before accepting. Each choice can also have repercussions later down on the game. Choices are exclusive, although once the game is finished, it is possible to make the other one through NG+ on the same save, allowing to get both bounties, and, save for a specific case, keep the recruits.

Warning: as this will cover every impact of Luka's choice, spoiler abound.

Alice or Ilias
The very first choice made by Luka happens right after he receives his baptism in Ilias Temple. The weakened versions of the Goddess of Light and the Monster Lord are at each other's throat. Both of them want him to join them to help them restore their true power, but as they can't bear each other, only one of them can accompany him. See here for the full effect on the story.

Special: Sonyaless
Recruiting Sonya can be skipped by directly leaving Iliasville rather than going to see the village elder. The impact on the story is minimal, as either Luka or the chosen deuteragonist will fill for her dialogs. However, the gameplay is greatly affected:

-Random encounters won't join you. Only story characters will, although Nuruko will be skipped too.

-The Pocket Castle won't be available. A change maid will be available in Ilias Temple to allow you to switch characters. You also can get neither the affection rewards nor the request scenes. You will still be teleported inside the Pocket Castle whenever Alice or Ilias calls for a strategy meeting, giving you a chance to do the above.

-As Sonya joining you is skipped, so is Nero's first encounter. Despite this, the characters will act like they've met before in Harpy Village.

-Since speaking to the Village Elder has been skipped, he won't give you the Storehouse Key, meaning that the items inside (and Remi) can't be interacted with. The key cannot be obtained, even after Sonya is forced to join you near the end of Part 2, so Remi can't ever be recruited.

-Luka can't traverse the poison marsh in the east part of Iliasville unless Sonya is in the party, meaning that not only can Lime not be recruited, the soldier won't give you the Soldier's Key that unlocks the chest containing the Proof of Bravery in the Cave of Trials, meaning that you lose access to the Guard Job and every other job tied to the line until Sonya is recruited.

-When Luka casts Holy Light for the first time on the Ilias route, it still manages to hit Sonya who's all the way in Iliasville, and Ilias comments on the distance.

-Luka can't wake up Lazarus unless Sonya is in the party, meaning that you can't progress in the Monte Carlo sidequest or visit the Don Father's Mansion during the events of Part 1. While the game takes never meeting Lazarus and Merlin into account later on in the game, the Monte Carlo sidequest is inaccessible, meaning that Eva can't ever be recruited.

-The Elf Princess event occurs as usual, just without Sonya.

-The stranded Polar Bear Girl doesn't materialize until Sonya's recruited.

Sonya and Nuruko will be forced into the party by the White Rabbit once Luka progresses to the Snow Continent. Doing so will earn the Sonya's Bizarre Adventure achievement.

Witch Hunt Village
When Luka arrives in Witch Hunt Village, the party gets involved in a conflict between Lily and Lucia. Most of the men in the village got killed by the women they oppressed after the latter group got given the power of tentacles. Lily wants to share the power amongst all the oppressed to give them the mean to fight back their oppressors, while Lucia is worried that it would just lead to more slaughter and prefers to keep its spread controlled. Luka has to choose who he will side with.

Both Lily's Mansion and the Tower of Magic can be explored, no matter who Luka decided to side with. The choice is locked only when you choose the option to start the boss fight with either of them after meeting them in their deepest sanctum.

Choosing to talk to each of them when they're in their deeper sanctum nets the player an achievement.

This choice later impacts Succubus Village.

Navy vs Fishy Pirates
As Luka needs to cross the Inland Sea to reach the northern part of Sentora, the Navy admiral, Leviathan, has the path on lockdown to prevent spies from reaching the Noah Region, and refuses to let civilians pass. However, she's willing to make Luka a Navy auxiliary if he deals with the Fishy Pirates. Luka is then approached by the Fishy Pirates who don't harbor malice towards anyone but actual pirates, and say that they will give them their support if he sides with them.

Leviathan can be recruited independantly of this choice. Both the Pirate and Marine jobs will be accessible as a reward as well.

Additional Navy Equipment (only if siding with Navy)

Plansect Village
The war has been reignited in Plansect Village by Tezcatlipoca and Quetzalcoatl. Queen Bee and her followers have been pushed back to Red Mountain, and Alra Priestess requires assistance to deal the final blow. Luka is free to side with either of them, or as the heroine senses that everyone is tired of this war, play peacemaker.

Succubus Village
When Luka arrives in Succubus Village, he's surprised to see succubi fighting each other. They're led by a vengeful individual named Natasha, who reveals that she wants to kill a man that raped her back in Luddite Village. He eventually reaches her when the demon reaches Succubus, who's protecting the man to give him a fair trial. Luka must choose between supporting either Natasha in her quest for revenge or Succubus to get the man judged fairly.

In both cases, Natasha ends up acknowledging that he's not worth killing in the first place and ends up living in Succubus Village.

Trivia

 * Several choice-exclusive characters have interactions, (Lily and Lucia, Succubus and Natasha), possibly hinting that NG+ has a weight on the story.