Well in the genre that I'm most versed at, Battle Shounen, they both have their strengths and weaknesses. Of course over use of the skill-pill can ruin a series' power scaling (Fairy Tail) but done right, it can resolve a problem and with the implementation of both limitations and drawbacks it can bring the concept to another level (Gear 2 from One Piece and HxH's transformation with Gon.) though the skill pill (or as I like to call it, the Super-Saiyan effect) always should have a plot relevance later on, should be done with high dramatic stakes and should always, be a result of or part of a character arc or change.
Organic Growth on the other hand, should always be the consistent way to go, and the Skill pill should be a result of this growth with a mix of the themes from the story arc. Organic growth is the Rising action of the character arc in battle shounen, Therefore, in my personal opinion the Skill-pill should be the climax of the character arc, if you use it at all. The key difference is, Organic growth should be a thing almost all the time and a skill pill doesn't need to be used at all.