The problem you mention is theoretical. Patent holders weren't doing that, so "solving" that problem isn't a win.
Patent holders were picking the most friendly of the large countries (usually Germany, sometimes the UK) and suing there. Germany and the UK both have specialised patent courts. Judges from these courts will be obvious candidates to sit on the new court. So the worst parts of the old system are going to become the rule for the whole of Europe under the new system.