[Lamont Cranston]

They dont have enough. Passenger numbers have been going up since the mid 2000s, and they have been lax in addressing this issue and thats why they brought those Hitachi back into service, but 7 geriatric trains hardly make up for what ought to have been 10 a year since 2004 or there abouts.
When they increased services at the end of 2008 without actually getting new trains, that simply meant there were fewer in reserve - and we saw what that led to when there were a massive number of breakdowns during the heat wave: the entire system colapsed.
But yes there are a number of external problems that make it worse:
time tables are based on the speed of the ancient Tait and Harris trains - all the current trains are faster than them but stick to their schedules, unless its waiting for a train up ahead to clear the line this will be the reason why a train is sitting at a station when its meant to go, making up the difference so it doesn't arrive early;
old signals & old tracks and tracks that need duplication - old signals or single tracks will be why it'll be slowing to a crawl or stopped waiting for another train up ahead to clear the line, old tracks mean slower and less frequent services;
the viaduct between Southern Cross and Flinders St - regardless of how many trains the Loop can handle (and that can spark a debate lasting hours), the bridge connecting these two major stations is too old and too narrow for any more trains and the development too close around it and under it prohibits tearing it down and building a new one.