What is the difference between a large country and a smaller country holding the EU Council Presidency?
Well, one of the differences is that smaller countries usually have less diplomatic representations spread all over the world.
Since the country holding the EU Council Presidency also fulfills this function in the different third countries - i.e. co-ordinating local activities of EU member states or representing the Council towards the state institutions - this means that a country which holds the Presidency but does not have a diplomatic mission (or that for other reasons is not able to fulfill the Presidency function) in a third country has to be replaced by another EU country.
In the case of the Czech Republic the quota is 64:83, which means that the Czech Republic is only represented in about 43.5% of third countries, in all other cases being replaced by other EU member states. That is why the function of the local EU Council Presidency is currently carried out by 14 more states (Sweden [next Presidency], France, UK, Germany, Italy, Spain, Poland, Portugal, Netherlands, Hungary, Finland, Belgium, Ireland and Denmark) and not only by the Czechs.
For a comparison: During the German Presidency in 2007, the quota was 121:26 (82.3%); during the French Presidency the quota was 133:14 (90.5%).
In fact, this is not a problem, and usually the smaller EU countries are still represented in all major third countries. Yet, it might still be that this sometimes complicates co-ordination and information flows, especially when there are unforeseeable crises in some smaller states.
But to be honest: In a common Union, does it really matter which EU member state's diplomats take the role of the Presidency?
(For the replacement procedure and the list of countries with the different local EU Council Presidencies check this recent Council document.)