The Fall and Ascension of Alexander Engel
The only pokegirl story I've read is A-kun's Crimson League stuff, so I'm not sure how much that reflects the rest off the stories, but in case it's accurate: This story contains little "taming". It only happens when it makes sense in the plot, and the first case (it doesn't even count as taming, actually) doesn't happen till chapter 5. So...yeah. More story driven than anything.
In addition, I know it's probably considered amateurish to give your main character many Bloodgift/Curses, but I couldn't help myself. Sorry in advance.
Alexander Engel was from a small town in the Crimson League where there was not a single pureblood human, and, like some people, as far back as he could trace his ancestry, all his maternal relatives were pokegirls. Because of this, just about everyone in Alex’s village had blood gifts, and about 90% of the males became Tamers, while a good 80% of the females Thresholded.
Alex had grand dreams. He believed that he was destined to be the greatest Tamer in history, to defeat everyone, tame all the legendaries, and be all around amazing at everything. This was due to his False Superiority Blood Curse, but even then, Alex was…headstrong. He set off as soon as he could, at the age of 16, confident in his skills.
Six years later, he is world famous- or, at least he likes to tell himself. In reality, he’s more “regionally known” than anything. He’s never met a legendary, though he’s as sure as ever that they’re around the corner.
In his travels, he has, on occasion, ran into a Rocket Lieutenant known as Darius, and most of the time, he has come off winning. Their last encounter, a few weeks ago, was the last straw. Under the pretense of being a scientist sending Alex off to an unexplored ruin in search of its treasures, Darius sets up an ambush for Alex. With a squad of Rocket Grunts, Darius beats the hell out of Alex, steals his harem, pokedex, and supplies, and leaves him for dead.
Well, not entirely for dead. As a parting insult, Darius leaves him a hacked pokedex with one registered pokegirl: A Feeblass with an…unusual temperament- yet still as useful as all other Feeblass.
Stranded in the middle of the jungle, with a more-or-less useless pokegirl and few supplies, Alex must return to civilization, find Darius, and get his Harem back, all while dealing with his new companion- plus the rest of the motley team he gathers along the way- surviving as barely-suppressed memories of his painful past are dredged up, and dark reminders of his own past failures return.
Alex has a long journey ahead of him.