Hi,
yes this is possible, you can use HTML delimiter field type and Content Plugin to make this, follow these steps:
- Make Skype field not available in profile page (it will be available only in edit profile/registration page), we recommend to use text field type
- Create a custom field of type HTML Delimiter and set it to be available only in profile page
- Set HTML description in the new field with something like this*:

<a href="skype:{user link_alias displayed raw}?call">Call Me</a>

- Edit Skype field and add this condition: if equal to custom value (leave empty custom value) then hide HTML delimiter field

In profile page you will see HTML field type only when link field is filled (condition), it will show the Skype link.

* NOTES:
- HTML editors like TinyMce (built in Joomla editor) should not recognize something like {user ...} as link, so it may change the output, so I recommend you to disable editor when you edit this field.
- in the href attribute you can use also something like "callto:" or "tel:" (instead "skype:" ), these are more universal and should works with skype.

Docs:
HTML delimiter field type: http://docs.easy-profile.com/index.php/article/html-delimiter-field-type
Content Plugin: http://docs.easy-profile.com/index.php/article/content-plugin