From a processor perspective, the Core i3-6100u would offer better overall performance. AMD APUs have pretty poor performance when it comes to the processor.
There are no benchmarks available yet for the Radeon R5 (Stoney Ridge) graphics core in the A9-9410. Based on specs alone, Notebookcheck.net, ranks it better than the Intel HD 520 graphics core in the Core i3-6100u CPU. However, that can change once if and when they start benchmarking laptops with the A9-9410 APU.
To give you an idea of performance you can click the following links to see benchmarks for the Intel HD 520 and Radeon R5 (Bristol Ridge) graphic cores. The laptops tested with the Intel HD 520 are all Core i5 or i7 CPU which higher clock speed so performance would a...