I've thought a bit about what makes games fun in general, as well as what makes netrunner fun in particular. I think a couple of principles intended for this game are:
1) The runner always has options
2) The runner can't use the same tool to solve every problem
We can see for example that Caprice is bad because she breaks rule 1 and Faust is bad because it breaks rule 2.
Now let's take a look at the history of recursion.
In core, there wasn't much recursion. If you were worried about key cards getting trashed by damage, you could just play them. If you were worried about program trashing, you could make sure you had a sentry before running, and as for Aggressive Secretary, you could expose it, or siphon the corp so they couldn't trigger it, or scout it out in central servers first.
In C&C, runners got a lot of recursion, and they were using it not as a reactive tool against corp damage / program trashing, but as part of their own plan, bringing back Parasites, SMCs etc. These recursion cards were too powerful (as evidenced by Clone Chip and Levy being restricted now).
What happened next was corps got more tools to attack the runner directly, but no one played them because they were weak against these recursion cards that runners were already using. Potential Unleashed and other milling cards could knock out things before you had a chance to install them. Chronos Protocol could choose which card you discarded.
We can already see that the recursion is breaking rule 2. No matter how the corp attacked you, you could solve it in the same way, with cards you were already using.
Then corps got even stronger cards like Batty and Hunter Seeker. These cards avoided being called out as unfair because of the powerful recursion the runner has, but they actually do break rule 1. The runner only really has one solution to these cards. (Milling agendas into archives or using Film Critic to avoid stealing agendas or using Councilman against Batty are some niche options but not something you'd expect many runners to have).
Imagine hunter seeker versus core criminal, whose only decoder is 3x Crypsis. Since the crim might have to steal four agendas to win, it's possible to trash every crypsis and lock the runner out.
Skorp isn't at fault. All Skorp did is shove these existing problems into the limelight. Make recursion weaker and make program trashing weaker. Then corps will use a variety of ways to attack the runner and runners will use a variety of ways to solve it, including having extra copies of their key programs.
Now let's take a look at the history of deck design.
The question is, was it always intended for runners to have spare copies of programs and AIs as backups, and why didn't that happen?
One thing is that at high levels of competition, the economy became very important. Having to use Crypsis instead of a real breaker was as good as losing anyway.
Also, runners were very aggressive. They ran without programs and tried to keep the corp poor. They used Parasite to trash ice. They also drew lots of cards. So runners used fewer icebreakers in their deck since finding them ASAP wasn't important, and corps used fewer ETR ice that was just going to cost them creds and get parasited, and more stuff that taxes or punishes facechecking, which meant that runners needed their breakers even less. The strength of R&D multi-access was also an issue because it meant runners didn't always have to worry about the servers the corps were scoring in either.
This relative unimportance of icebreakers seems surprising from an intuitive / beginner's look at the game. You expect that icebreakers will be the most important cards in the game and that getting them out is every runner's first priority otherwise corps are free to just score out their agendas.
Perhaps, now that parasite, credit denial, oldschool criminal, and r&d multi-access have rotated out, this will become true again. Looking at the original post, this was called "inefficient deck building". You don't want to just chuck two extra fracters into your deck, because that was never the way to play under the old rotation. But if it became the new standard then you wouldn't feel like you were teching against Skorp specifically.