Great question, not just for Twins fans, but for what the HOF should be. I think the greatest players at the various positions/roles in each time frame should be represented.
There of course is no magic formula for how long or how great you have to be, but Santana was belatedly promoted to the rotation in summer of '03 (classic Twins move) and pitched so well he finished 7th in Cy Young, then was top 5 the following 6 years with 2 crowns and could easily have had 3 or 4 (look at how comparable his 2008 season with the Mets was to Lincecum). On top of that, he was excellent as a post-season starter with one bad inning (game 4 in 2004) out of 5 starts -unfortunately the rest of the team didn't hold their weight. He and Halladay were the best pitchers of that time with Halladay a first ballot and Santana doesn't get past the first year. So he's the bigger snub to me.
That being said, Nathan was one of the very best at his role - relief pitching/closing out games under pressure. Mariano was his own level, but after that Hoffman, Wagner and Nathan were all excellent. Hoffman did it for longer, so he's in. The difference between Wagner and Nathan is so close so why will one get in within the next two years and the other is dropped off the ballot after one year? Also a snub. Right or wrong there are levels of induction: near unanimous, first ballot, inducted years 2-5 gaining momentum each year, made it but was forced to sweat it out, veterans committee, waited until he died. Eventually Johan and Nathan could get in.