I believe Cyprus is destined to remain divided between Greek and Turkish factions. The United Nations has tried for many years to get the two sides to come together and form an agreement that would allow for the dissolution of the division between them. Talks have never been successful. It appears that Cyprus is destined to remain divided, just as Berlin was.
The Greeks and Turks have been in dispute over the capital Cyrus for a long time the city is divided by what is known as the Greenline, they are in what one might call a negative peace there is no violence but they definately are not in any agreement for now or anytime in the future. The Berlin Wall held may of the same characteristics as the Greenline. Berlin was seperated into an East and West side with guard towers this became known as "Anti-Fascist Protection Rampart". These two cities could not find a way to see anything other than their own views requiring them to cut themselves off from what they couldn't understand.
No, I do not think that the Cyprus dispute of today can be compared to a modern Berlin Wall. These are two very different topics, and do not relate to each other enough to warrant them being labeled as the same event just happening in different time periods and places.
Although there are similarities between the Berlin Wall and they buffer zone in Cyprus, the two dividers served to divide their respective countries for different reasons. The Berlin wall separated East and West Germany for political reasons. The people in the East where governed by Communism, and in the West they were largely democratic. In Cyprus the dispute between the North and South is based on ethnic factors, the North are mostly Turkish people, and in the southern part are the Greek people.
The Berlin wall was a focal point of international politics and diplomacy for decades - people study the conflict around the wall in history classes down to the middle school level, and it came to symbolize the differences of an entire era. Cyprus is a tiny blip in history overall.