The problem does not depend on Skype per se but in the order of merging so:
1) if the first contact does NOT have Skype data inside, merging with a contact WITH Skype data goes well;
2) if the first contact HAS Skype data, the app crashes before letting me choose the other contact to merge.
The merge worked well in case 1) with a contact which contained various information, including email, MSN and Jabber (I don't have Facebook, Twitter nor Whatsapp) so in my case the only difference is in Skype data present or not in the first selected contact.
EDIT: if you merged two contacts and the resulting one contains Skype data the merge still works well, so if you have 3 contacts of which 1 with no Skype data and 2 with Skype data, simply merge selecting the former as the first one and then you can merge also the third after the first merge