The Templars' advantage over the Assassins seems to stem from the fact they're usually occupying positions of power though, whereas the Assassins tend to be the underdogs. There's not necessarily more individual Templars than Assassins at any given point in time (besides during 2012, of course), it's just that the Templars have a lot more influence than the Assassins do.
There were just as many Assassins as there were Templars in AC2's cast of characters, for example, but the Templars were led by Rodrigo Borgia, head of one of the most powerful families in Europe, whilst the Assassins were made up of prostitutes and criminals and led by a Mercenary Captain.
''Snake from Metal Gear 2 owns everybody. Because he used an owl. To make a guard think it was night time. In the middle of the day. That's just hardcore''