Now that i've gone through it all, here are my thoughts.
>>430107991. Great, and my favorite of the bunch.Possibly the most PMD-like plot of them all, feels like something TPCi would've made. Almost like a natural evolution of sky's plot.
>>430108132. Solid. Love the idea of the partner being a far cry from the sappy but dedicated little chickenshit we seem to get every game.
>>430108393.Awful. Convoluted and incoherent. I do like "armour clad knights" as a theme but this story just feels really silly, even for a PMD type story.
>>430108514. This concept does not fit with pokemon at all. I wish I could elaborate but I just don't like it.
>>430108685. I like parts of it? I love the setting, and I love the idea of your partner being a grifter who slowly develops into a good natured person. I really don't like Cypress as a villain though.
>>430108856. I like the concept a lot, it's a lot more well developed than 4 as a "PMD+advanced technology" type story. I do think you could simplify the story a bit though.
A lot of the appeal that adults find in pokemon is in its relative simplicity, even with the story. I don't want there to be points where an evil villain faces you down and dumps a bucket of exposition on you before an underwhelming boss fight. It's still possible to have hard hitting emotional/heartfelt moments without a final-fantasy level story, just look at PMD sky.
Like I said, good job OP. What are you planning to do with it though? Are you planning to create a fangame? I know PMD fangames are rare so I'd love to see one with some of these ideas.