It takes longer, especially when you’re first getting started and you’re not in a rhythm. You can find lots of good recipes that don’t require manual kneading, but you still have to set everything up, measure it out, and pay attention to rising times.
There’s more work involved: again, kneading, watching rising times, etc. (most recipes really aren’t much work, however, so don’t let this scare you—it’s just more work than going to the store and banging a loaf on the register counter)
Clean-up…’nuf said
The most important one: consistency. Home-baked bread (or anything, for that matter) doesn’t always turn out the same…especially when you’re just getting started. With practice and repetition you could become an expert, and make the perfect loaf of bread in your sleep and it will taste the same every time. But baking bread is a delicate art as well as a science. The end result can be impacted by weather, temperature changes in your kitchen, the functionality of your oven, the number of seconds or minutes you spend kneading or mixing the dough, the quality of your flour. So while all in all, with a good recipe, you’ll get a good result every time, you might not expect to get the same result every time.