Having both I can tell you there's some differences you have to pay attention and decide what is most important for you.
The first and foremost difference is the trigger. Although you can have improve your Glock's trigger with nice polishing or even spending some money to handle the over travel (or lots replacing it completely), it most likely won't turn it to glass rod breaking trigger. Is this important? Most likely not, and as Cancer wrote there's a learning curve and you will master it over time. So, boils down to preference and in my case I prefer a crisp, glass rod breaking trigger.
Secondly, comes ergonomics. Buying a Gen 4 Glock helps to tweak it to the size of your hand but the grip angle is different from the CZ, so you will need some time to get used to it. Also, being mainly metal made, CZs are heavier than Glocks and it seems to me the recoil is a little bit smoother, which my wife (she hates the Glock) and I prefer.
From the accuracy perspective, both guns are more accurate than me but in my hands the CZ does a better job shooting tighter groups. It could be related to the weight (better recoil control) and the way the slide is attached to the frame. Glock has a couple of contact points whereas the CZ is continuous.
Last but not least, accessories. Well, here Glock is the winner hands down. You will be able to complete transform (to a cost) your gun much easily than a CZ (which also is quite customizable). However, it boils down to your decision about spending money tweaking the gun. For some, customizing a gun brings as much pleasure as shooting it
Being honestly, my Glock 17 was the first handgun I ever used, so it has a place in my heart and I am keeping it due sentimental reasons. The CZ seems a better fit for both my wife and I.
LC