We made the decision based on a few factors. All the clinics offered pretty much the same services so it came down to a few variables.
Firstly price: cycles in Prague were more expensive, accommodation in Prague was more expensive, food in Prague was more expensive, things to do in Prague were more expensive, so generally you get the idea.
Secondly atmosphere and relaxation: Cycles don't work, apparently, if you are stressed out. I have a penchant for not stopping and find it hard to relax and wind down. I kind of thrive on stress and being busy. We knew if we were in Prague that I would not be able to stop myself from going out and being busy which might not have been good. Zlin has a slower pace and is generally a lot more relaxing, the town has things to do but it's not so hectic and that suited us. We had been to Prague before and based our decision on that. We like Prague for a day or two but not weeks.
We also considered the wait time and if the clinic could schedule us when we were able to travel.
Lastly, we contacted a few clinics and you really need to go with your gut. Who do you find you are connecting with or feel comfortable or happy talking to? I got a fast response from Zlin compared to some other clinics and I also found some others far less personal. Everyone is different and it's such a big thing that you are doing so you really need to use your instinct and go where you feel suits you best!
I hope that helps