Respectfully, and I definitely don't mean that my way is the only way or anything like that... I like to use JFETs for certain applications because the particular JFET I'm using has a characteristic or response that I really like. I don't personally feel that MOSFETs and JFETs and, while we're at it, op-amps, or just regular transistors, or diodes of different kinds will fill the need for every circuit.
You take something like ZVex's SHO and it's a very slick design, you can see why he used a MOSFET there and it does sound good and work great in that circuit. But there are a lot of other possibilities for making a boost or drive where JFETs are a great choice, or I'd want to use a specific op-amp. And speaking as a builder who has been really fortunate and blessed to experience growth to a scale where selection does start to matter, honestly we haven't had any trouble as far as making sure we're using parts that are within tolerance, even though we have tight tolerances for our pedals since they have to be the same pedal to pedal for pros who don't leave home without a backup or two. (For example, you never know what's going to happen on the road... Beer can ruin a pedal's day pretty quick, and if it's part of your sound, you have to put another one where it was for the gig tomorrow, and it can't sound different).
It's just a matter of picking the right part for the job, first and foremost. An "ears" thing as much as having electrical knowledge, sometimes you take an engineer-like approach and sometimes you can just tell that "for this pedal, this part is necessary to get it to sound right."