In the old days there was also inflation, even though gold was used as currency. The increase in the gold mine´s production (and furthermore, the possibility of everyone being able to suddenly convert their gold into currency) affected the inflation just as today's money. If you consider that the central banks now decide when to create new money, you will see it is easier to control inflation and any other type of economical problems, by the use of it´s monetary policies to prevent them. About your gold or silver into certificates idea: it´s currently done, and it wouldn't change at all any problems: the banks could make the same operations they do now with paper money, because they turn the gold or silver into paper money.
Another problem gold and silver have is that if their reserves don´t grow with the economy (which means there isn´t enough of it for transactions), then they would necessarily be turned into paper currency to stop the problems, which would make everything be exactly as it is now.
I think that reading Adam Smith´s "The wealth of Nations" would explain this better than I possibly can right now. What I believe that is today´s problem is the lack of regulation, not the currency.