The i3 has a higher stock speed, so in single threaded apps requiring the use of 1-2 cores, the i3 will be stronger than the i5. The i3 also uses HyperThreading which will run 4 threads simultaneously same as the i5. While this can be slightly slower than a full 4 cores in very heavy load applications, for most apps the i3 will equal or exceed the i5 as per core usage is not high enough to impede data flow.
Then there is also the added advantages Skylake has over Haswell cpus. They run cooler in general, most times needing nothing more than the stock cpu cooler for decent temps. The i3 can be OC'd slightly using the BCLK method, not recommended on the i5. Upgraded audio, usb3.1, m.2 ability, native dx12 compatability etc. Also, the i5 has only 1 possible upgrade, to an i7 or Xeon v3 cpu, which for the most part will not show any real performance gains other than in games like bf4 which take advantage of all 8 threads. The i3 can be upgraded to either an i5 or i7 if you need stronger thread usage. However, the i3 6100 remains the best bang-for-the-buck Skylake cpu on the market.