These parts that become "the part" often have this issue relatively early into the lifecycle. The 741 op-amp is another example. They are often bad and expensive, but they are a default so people put them in.
replyIn fact, unless ubiquity in availability is a really core part of the design requirement, they almost certainly aren't the right part for the job.
replyMost parts in most designs aren't anywhere close to being specification-critical. Specifying the 3904 is a great way to say "I need an NPN transistor here, and it doesn't really matter which one" (because, oh man, they can ship a lot of different things in that "3904" bin spec, and they do). So the "jellybeans" are often ideal choices.
replyWhen they are not, that is when the design engineer earns their pay.