As others have pointed out, there were many factors why 727 ended up as a trijet. Engines were a big one.
Simply stated, had the latest and greatest (and newest) variants of the Pratt JT8D (-15, -17, -17R, -217, and -219) actually existed when the 727 was designed (instead of the common predecessor -1, -7, and -9 variants, all with less thrust), who knows what would have happened.
Now that the 727's are long-since paid off, and the engines (most of them) upgraded to at least the -15 variant as a standard, the 727 still has a cost-effective future in most cases. Compared with a new aircraft, a well-maintained 727 still is good value, even with the 3rd engine and crewmember.
Now, if Jet-A goes to 2 or 3 bucks a gallon for airlines, that could all change in a hurry...
ALL views, opinions expressed are mine ONLY and are NOT representative of those shared by Southwest Airlines Co.