difficult to answer without seeing what system you have at the moment. i'm presuming that you are ulgrading rather than having a system put in for the first time?
whichever you opt for your going to have to have a condensing combi or system boiler. if you go for the system boiler you may have to have your cylinder upgraded to one with a high heat recovery coil if you dont already have one. you may have to have your controls upgraded to comply with the boiler interlocking regulations and its unlikely but if you have gravity hot water you would have to upgrade to a fully pumped system, all this adds greatly to the cost and is why installers like to opt for combi boilers.
saying that, a traditional system would give you a much greater flow of hot water unless you plumped for a very powerful combi or one with a water store.
i would guess that the system boiler would be cheaper to run as they don't need to be as powerful or burn as much gas.