The answer is pretty complicated.
AMD APUs do have better integrated graphics than, for instance, a Core i3 6100. If you were to buy the system and never upgrade it, the AMD APU would be a fine choice. The problem is when, down the road, you want to upgrade - socket FM2+ has no faster CPUs, and the CPU portion of AMD's APUs is pretty weak. With the i3, you can add an i5 or i7 later on.
If you add a discrete GPU, you're also much better off with a Core i3, because at that point you're not even using the APU's only real selling point, it's better integrated graphics, and you're left with a slower and more power hungry CPU that can't be upgraded.
So, I might be tempted by the APU if I were to build a small form factor machine that will never a video card, due to case size, but otherwise I'd probably pick Intel.