In a lot of ways, Simpson was a superwoman. Her 3:59 looked like an outlier performance, but then she backed it up by winning a world championship 2 years later, and backing that up with a number of medals in the following years. I don't know what spikes she was wearing when she ran 3:59.
Interestingly, 2009 was around the time the original Nike Victory was released, and we started to see an increase in 3:55-3:57 indoor mile times during this period. Waldrop's 3:55 record stood until this era, before guys like Batty and O'hare started chipping away at it.
With the current era, it is hard to determine all the factors leading to the improvements. Are Gary Martin and Ethan Strand actually 6+ seconds better than everyone who ran before 2010? Is a recently graduated Adam Fogg 5+ seconds better than the entirety of NCAA runners prior to 2010?
When you have 30 runners per year running faster than anyone ran in NCAA history up through 16 years ago, a number of factors are at play. Spikes, bicarb, running at fast tracks in fast paced races, different training, etc - all of these play a role. Even with increased interest, I don't think the talent pool has been a huge factor in the improved times. I imagine if all the NCAA runners in history between 1965-2010 were put in today's competition (with maybe a year to adjust to training), we'd see huge numbers running between 3:47-3:54.