My personal experience.
I have been making a chiltepin salsa that people rave about for the past three years. Everyone wants the recipe, which I've given out to no one!
Last Spring, I purchased four supposed chiltepin plants from a huge local nursery here in Tucson (and other chilies that turned out different than what the label said!), which turned out to be pequins, not chiltepins. I also purchased two chiltepin plants from Tohono Chul Park's nursery, who's chiltepins come from seed from the Baboquivari Mountains in Southern Arizona.
I had read that Chiltepins have a quick, sharp bite that fades away quicker than normal chilies, and that has been my experience. I had also read that Pequins take a little longer to hit, but the heat lingers on much longer than the chiltepin.
So I made two batches of my chiltepin salsa, first batch with chiltepins and second batch with the same amount of pequins (in grams). There was a world of difference between the two! The heat of the chiltepin salsa is almost instant, while with the pequin salsa you have to wait a bit to feel the heat. I also found the chiltepin salsa to be a bit hotter than the pequin salsa, but that could have been due to a variation in the heat of those particular chilies.
Both are good peppers, but I BY FAR prefer the Chiltepin! Too bad there's a severe shortage of them this year.
That's my personal experience.