This is a different question than whether he should be a Hall of Famer. There have only been 4 starting pitchers (as opposed to pitchers who were primary relievers or a hybrid like Dennis Eckersley) who started their career after 1965 and were elected to the Hall of Fame.
Nolan Ryan (1966-93): 324-292
Don Sutton (1966-88): 324-256
Tom Seaver (1967-86): 311-205
Bert Blyleven (1970-92): 287-250
Over the next few years, there will be 3 more pitchers who will almost certainly join them: Greg Maddux, Tom Glavine and Randy Johnson. There are some other pitchers (like Mike Mussina) who may have a shot eventually, but they won't get in on the first ballot. The one exception might be Pedro Martinez, who had a career record of 219-100 and won 3 Cy Young Awards.
With only 203 career wins, it didn't look at first like Halladay would have a shot to get in for a long time. After looking closer, though, I think he has an excellent shot. For starting pitcher to make it to Cooperstown with only 203 wins, they need to be truly special. No, he's not Sandy Koufax or Pedro Martinez, but he's a career different case from the large number of pitchers with around 200 wins that didn't make it.
His W-L% (.659) and ERA (3.38) put him well above pitchers with similar win totals that didn't make it to Cooperstown like Orel Hersheiser, Vida Blue, Bob Welch, Kevin Brown, Charlie Hough, Mickey Lolich, Jerry Reuss, Jerry Koosman and Luis Tiant. The number of pitchers with 200 wins and a W-L% of over .650 is very small. This alone should get him into the Hall of Fame.
200+ W, .650+ W-L%
That combined with 2 Cy Young Awards and 2 second place finishes should get him into the Hall of Fame, even if it isn't on the first ballot. The game has also changed so much in the past few decades that it isn't realistic anymore to have a magic number of 300 wins for a starter, but that doesn't mean that it will change immediately. While his win total will be an obstacle, I think that Halladay will have plenty of influential people pushing his case in the years to come and that his case is strong enough that he will make it into the Hall of Fame.