I lived in Cyprus in 2012 and that bail-in indeed caused issues, BUT keep one thing in mind; having a company there is one thing. It doesnt mean that you have to bank there. All companies that had non-cyprus banks were not affected. It's in that sense always better to never bet on one horse
Re substance and presence; just keep in mind that those requirements are everywhere and if they are not yet enforced that will change over the next couple of years.
Pick a place where you would be able to fulfil the substance / presence requirements yourself. Especially if your numbers are not high enough.