Edit: Obviously there are many, many positive factors and strides that Pakistan its society has made. But you came here looking for the negatives, so that is what I gave you.
The question can be broken into several bits.
Starting off with education, and why the literacy rate is so low.
Quite honestly... I don't know why but I guess it's simply not taken seriously when really it should be a national emergency that 40% of children are out of school. That's a national emergency, and education should be top priority.
- There have always been other concerns in Pakistan which have taken the mainstream media and opinion, both public and government. Such as military, militancy, terrorism, corruption, politics, poverty, religion, public welfare in terms of housing, food, and so on. So this issue of education has never ever been at the forefront ever, unfortunately. I don't remember the last time education was taken as a serious issue except Pakistan's spending on education is just short of 3% of the GDP, and that is embarrassing.
- A lot of people in Pakistan are poor, specially rural parts which actually constitute the majority of Pakistan's population, I think. So, families consider it a time waste to send their children to school to study for years, and instead have them working the traditional labor from an early age. Some simply can't afford.
- The literacy rate of girls is lower than that of boys, and this is a problem because of the traditional societal roles that are assigned to and expected from them. Since they're going to marry off, take care of the house, and do the household chores, people don't send them to school and drop them out before college. People don't realize the value of education when it comes to bringing up a new generation.
- If you see the percentage of children out-of-school across primary, secondary, higher and college levels, you will see that the percentage successively grows. The reasons are a mixture of the above two; that is they're considered a time waste, require financial investment, gender roles are at play, and so on.
Pakistani people being less liberal and less into versed conversations regarding Science
Well, you might just need to update yourself because in terms of lack of liberalism, our neighbor that is India is overtaking us right now. They've grown more intolerant than us, and that is observable from social media where you usually expect to find a generally more liberal and secular view, but in India's case you will find a large, large majority just growing more and more conservative about their country and open in hatred against Islam.
Anyways, just a general point I wanted to mention. Back to Pakistan. Pakistani people are indeed less liberal and more conservative to their viewpoint, and also less likely to hold versed conversations when it comes to global affairs and science. I think there are actually two segments of society now. I will go into depth in my points below.
- During the 1980s, General Zia, a military dictator, initiated policies of Islamization which pushed in a lot of elements of what people regard today as Sharia Law (I say today because I don't think Sharia Law has ever been properly defined, and interpreted, every country, and point in time, has seen different versions of it) wherein the education was affected, news channels and soap operas were affected, work attire was affected, and there was propaganda all around for its implementation; these Islamization policies introduced a new mindset into the people which was a bit extreme. Religious scholars were given an upper hand and more power, and they used this power to influence people, weed out those who did not agree, and such. This mindset, and infiltration of extremism into society, has lived till this date.
- That was the historical perspective. Now to the present. Even today, the religious scholars are very, very highly regarded, and can close the country at a whim. They exercise a great influence over the Government, and have only grown more, and more, bold each day. To showcase this, recently during the PTI government, TLP staged a protest over a major Supreme Court case. In it, one of the group's leaders openly said that the Pakistan's Chief of Army Staff, and the Prime Minister of Pakistan, are 'vajib-ul-katal,' meaning it is legal to shed their blood, Islamically... and they had many supporters... during every Government in the last two decades, these people have staged protests which have shut down the entire country and stopped it. In the political ground, they exercise influence but not presence. If that makes sense... they have this influence and ability, but they never get seats in the Parliament from votes of the people.
- Now, more generally, Pakistani people really love Islam. They really love it, and there is nothing wrong with this love. The issue is that they want it everywhere, and believe it is the solution to all problems, there's sort of this underlying mindset. It should be strict, present in your clothing, education, government... everywhere. This is the result of Zia's Islamization policies, and well how the general global dynamics are right now with Iran and Saudi Arabia. They think it's part of Islam to enforce these by law. And somewhere in between with the war on terror, new interpretations, and due to power of religious scholars, these ideas have crept in.
- Pakistani people really love Islam, and now here's a big problem. Anytime there is some injustice against Muslims or the religion in general, people feel that the religion is in danger and they need to hold more strongly on to it! Let me tell ask you, a half century from now, how 'Islamic' were exactly the Muslim countries in the Industrial age... they were progressing very normally, then the whole War on Terror, new interpretations crept into society, and people felt Islam is in danger and so on. If today there was no injustice against Islam and Muslims, believe me, the very state of Muslim countries politically would be very different. People are more comfortable with discussing ideas that are their own and in between their people, they value it and don't want outsiders criticizing it but are okay with criticizing it themselves, but when outsiders mock it, they feel they must protect it. That's how it is.
In regards to Science, that again has to do with education, and the fact that the topics which have always hit the mainstream media and opinion, have never been education or science.
Regarding English language
Now even though, Pakistan has one of the highest English speaking populations, it is not spoken correctly to say the least. There are some pretty ordinary reasons for this.
- Public schools never enforce an english-speaking environment. Essentially, the entire language medium is supposed to be in English save the Urdu and Islamic classes.
- The teachers are not up to the mark, their own English is questionable and not correct.
- Inter and Matric exams (Pakistan's higher education board exams) allow you to study the subjects in either English or Urdu, you can write your answers in either, naturally people choose Urdu. I don't know how accurate this is, I know this is a thing in rural places though, I don't know about Urban places.
- People just don't take it serious. I have learned Turkish, Russian and German, and although I learned English naturally from a young age, learning new languages really opens up how difficult of a language English is to learn for new learners. There are no definite rules in it everywhere since it has been so globally influenced and changed, it is a really difficult language. So, when people don't take it serious, they end up with broken English skills.
The Pakistani Bubble
This is very true, funny enough. However, I am not sure as to why myself. I recon the answer would be seriously long, and this really requires an analysis of society and opinion, and also historical perspectives; like Pakistani people really love Islam and believe they're divinely chosen to defend it. I am sure what I mentioned plays a part in it. What I do know however is that there are major Youtube channels with millions of subscribers which propagate and expand this bubble, like Haqeeqat TV which says that vaccines are a Jewish conspiracy by Bill Gates to make our people infertile, and such stupidity, and millions of people believe the guy. So, there is indeed this bubble. I don't know why, but in essence due to lack of education and scientific importance, that is obvious.
My opinion about Liberalism, Secularism in Pakistan
Due to the Governments' horrible policies on education, and lack of progress to improve the education system, merit boards, and the examination systems; many, many people have opted for private education, and the Universities have largely kept themselves independent of the Government. As such private institutes and Universities have been providing a quality education. But more importantly, these have opened up free spaces where people can discuss ideas and concepts, and due to the failure of conservative policies and Islamization policies of all Government, it has given rise to more liberal and secular views, quite rapidly, in the more privileged circles. Maybe, this will be a factor many years from now.