The lighting is hard, directional and not very flattering. There are hard shadows giving the whole scene a very sterile feel. There's also white balance issues with a great deal of yellow to the overall colour. Was that plate white?
Why not use natural daylight from a window and a reflector to bounce light back into the shadows? Results would have been softer light, easier white balance, and a more attractive feel to the overall image.
The black table cloth is not helping I feel. The overall darkness of the image is not really matching the subject and the patterning of it is a distraction. The cupcakes are light, fun, cheerful, yet that table cloth is sombre, dark, serious. Try to use something that enhances the "feel" of the shot. Why use lighter pastel colours for what they are sat upon and capture a more cheerful atmosphere?
The chocolate flapjack things look very messy... made worse by the very hard, sterile lighting. Softening everything down with diffused lighting would help here. The hard lighting has made the messy unattractive, whereas softer, more diffused lighting would have made is more appealing. You say you wanted the home baked, hand made feel by leaving them messy, but nothing else about these image re-enforces that "feel". They feel like police forensic evidence shots rather than inviting, soft and "home baked". Again, a lighter set, with attractive, lighter shades and hues.. soft natural light from a large window, and large white reflectors on the dark side of the set would bounce light back in lifting the shadows to reduce contrast.
Good photography needs good lighting. Good FOOD photography not only needs good lighting, but great sets that re-enforce the feel the food demands. Eating is not just something we do to refuel our bodies, it's a social event, and mood is very, very important.
This image uses colour well to enhance mood and feel, and it also appears to use very soft, diffused lighting. This is probably just diffused daylight, and if it's not, it could easily be recreated by using diffused daylight from a large window and a reflector.
Look how
this shot uses the surrounding scene dropped out of focus to give context, meaning, atmosphere... makes it an attractive, domestic setting. Why not try this with your cupcakes... think of colour used, setting, context.... use colours more cleverly to make the viewer feel something about them. Look how the colour of the background in
this shot compliments the cupcakes in this shot. Yet the shot is simply diffused daylight.. shallow depth of field... in fact, the only difference between this and yours, is the lighting used, and the colours, and the fact that it's in a "setting" to give it context that marches the intended "mood". It's not perfect... none of these images are... I've just pulled them from a Google image search, but they make the food look a LOT more attractive.