These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Base Breaker: Ao. People either love him for his personality and for the fact that he truly cares about Shino (some even preferring him over Sousuke), or hate him due to his actions towards Sousuke and stealing his bead, as well as messing with the lives of a few other characters.
Ho Yay: The manga originally ran in a magazine that catered to those interested in Boy's Love; aside from implication, pokes and poses, however, it has yet (at least in the anime) to travel further into the territory, keeping more of an action-adventury tone overall—which was perhaps the justification used when it switched to a new magazine.
In episode 4, after Kobungo suggests that Genpachi start to live again, he tells him he should find (a marriageable) someone for him who's "strong-willed and seems practically immortal." Genpachi says the only person he knows like that is the older sister at the market—until suddenly Shino pops up above him, asking if he's okay. Then he stares up at him for a minute, and says dead-on, "I've found one." He states wondrously that Shino's exactly his type and that he'd be willing to wait a few years for him to grow up, to Kobungo's insistent wailing that Shino was a man. Later Kobungo tries to bring Genpachi to his senses but concludes that 'he's lost it'.
In episode 8. Sousuke, Shino, Genpachi and Kobungo board a train. Genpachi tries to go in after Shino, but Kobungo stops him. This hilarious scene ensues:
Kobungo: Bro, where do ya think you're goin'?
Genpachi:(innocently confused) I'm going to sit with Shino and -
There's also teasing for Shino/Sousuke: Sousuke's devotion to Shino, his jealousy towards Rio (foot grabbing anyone?), Shino sitting/lying on top of him, calling him cute, Ayane walking in on them and hurrying off blushing and apologizing.
This seems to be reinforced further in season 2, albeit in slightly heartbreaking way: in the final cut of the opening video, Shino attempts to reach out for Sousuke only for him to break apart in the end, while the ending video has them spending time together. Whether they are Foreshadowing or Fauxshadowing over what may happen in the future remains to be seen.
Their relationship is the main focus for the last three episodes. Sousuke falling unconscious sets Shino on a frantic search for his bead, and even after suffering a deep wound he gets back up and tries his hardest to resist succumbing to it as he never got a chance to apologize to Sousuke. There's also the both of them having flashbacks of the times they spent together (during their childhood and from earlier episodes), Shino's promise that he would never leave his side, Sousuke standing up to Murasame to bring Shino back to his senses (which nearly got him devourved by Murasame), and the constant shouting of each other's names throughout the last episode.
Shino and Sousuke's shadow, Ao. Ao cares for nothing else but to complete his body so he can be with Shino, and goes to great lengths to do so. The ending theme of season 2 does a good job of showing just how much he wants to be with Shino, but he keeps at a distance. Mostly because Sousuke is with Shino both times he appears.
Ao is definitely not happy that Tamazusa wants to use Shino as a vessel for her child and screams in agony when Shino collapses from his injuries.
As soon as Tamazusa is distracted, Ao grabs Shino and holds tight to him through the ensuing battle, fighting one handed until Murasame goes berserk and forces everyone away from Shino.
Kobungo apparently crushes over Keno, although to his defense, he is dense enough not to realize that Keno is a guy. Whether Kobungo still crushes over him after the events in episode 11 has yet to be seen.