Both are excellent compact SUVs with potent and punchy 1.0 direct-injection turbocharged petrol engines. However, which one you choose depends on your preference, and there are pros and cons to each.
Comparing purely engines, the Hyundai is slightly smoother, though the Skoda has more punch, despite its lower power figure on paper. Assuming you choose the manual gearbox, both are smooth shifters with light clutches. If you choose the automatics, the Skoda's 6-speed torque converter AT is smoother overall than the Hyundai's 7-speed DCT, but it can feel overly eager moving off from a standstill.
On features, both are well equipped and represent good value, though overall, the Hyundai has more. The Hyundai Venue is lighter and easier to drive, but the Skoda Kylaq is more engaging and fun. The Skoda has the slight edge on ride comfort, in case that is a priority. 
