Well, you see, back in her first appearance, Fionna was skinny to fit the more shōjo-style aesthetic of her episode. This was later changed by the crew in an attempt to make her less sexualized by the fandom. With even the slightest bit of hindsight, you can easily see why that's one of the most misguided decisions you could make, seeing as half the internet are now into chub characters.
In the current year, the dichotomy is only exacerbated due to Fionna and Cake's main audience being middle-aged women going through a mid-life crisis, so her being out of shape is done so the target audience can self-insert more easily.