I got exactly the same thing happening to my 97Legacy.  When going from a stop, the engine coughs for a sec and as RPMs go up, it's back in business. 
My knock sensor died some months ago so that was replaced.  I replaced spark plugs, air/fuel filters and 02 sensor but nothing helped.   When i disconnected the battery a few months ago and cleared the ECU, i think that was went away for almost a week but then the hesitation and rough shift from 1st to 2nd came back too.   
Oh well, will have to live with it. 
  
Quick question:  
How does one use a timing light? do i have to have the timing cover off to get the reading? 
  
Thanx