I felt that the system should, and will stay.

I am not a scholar myself, and if I enter civil service, I will be a farmer. Though the ideals of paying equal for same job scope is enticing, we have to consider the potential for career progression. It makes sense for organisations to expedite the career progression so that the talent will stay and also contribute to the company by paying them more money.

Have you guys seen the video of the monkey who was paid unequally? Here's the link for those who hadn't. 2 Monkeys Were Paid Unequally - YouTube
This is exactly what is going on in our society. And biologically speaking, it isn't wrong. Why should scholars doing the same thing be paid more than me? It's only human that we think about this.

However, often we cannot look at things from our perspective. Let's now look at things from top down approach. How is a company going to get a top talent? Assuming that people often perform their best in their thirties, it makes sense for me to rope them in in their twenties. Oh, I also realised that top talents seems to be good in studies. Should I inject money for their education? Yes they should. Hence, the origin of scholarships. It started from a rich company trying to rope in top talents. It realises that it's management never started from the bottom and it's racking its brains on how to get a person to start from bottom and rise up to the management. Hence, the starting of scholarships. Governments and other companies have followed as well.
As mentioned earlier, the last thing a company want is for their identified top talent to leave the company. As such, they will inject monetary awards and expedite career progressions.

We may often point out flaws based on our own observation. "hey, look at A, scholar only know how to study don't know how to work". However, I do believe it holds some truth that if someone is able to get theoretical concepts quick, he/she can learn things fast as well. I had been to scholarship interviews, and though I didn't receive the scholarship, I felt that the system was a good gauge of getting sharp minds. The hit rate is high. In a governmental scholarship, one is being assessed on many things from intellectual level, to capacity to imagine (spatial awareness or something), situational awareness, and also to get past, he/she will at least have a certain level of social skills (it takes more social skills for one to wayang than to be genuinely sociable) . The system is a good assessment, hit rate is highest among many methods a company have considered, but it will never be a hundred percent hit rate.

My question is, are we going to fault the system on it's occasional misses?

Instead of endlessly disagreeing, I urge more people will learn to think critically and think of concrete solutions. What would YOU do to change the situation? What can be done?

If you have no answer, shut up and start working.

I will bring in the example of politics to explain my point. What would you do to improve the situation in Singapore with a growing xenophobic culture?
Once you get the solution, congratulations. You have my support for election. If you run for marine parade, I will move house so I can vote for you.