Does an advisor owe his/her student anything? Will an advisor keep a PhD student only out of pity? I know what imposter syndrome is. But, believe me that's not the case with me. I have worked hard for the 4.5 years of my PhD, but I feel that my research is absolutely mediocre and as a result my self-confidence has taken a toll.

Now, my advisor is a brilliant person. She is well known in her field (computational mechanics) and has many high-impact publications (IF>10). I had my undergrad in materials science and was exposed to computational mechanics in my masters. I was fascinated by it and wanted to study and work on it. However, when I joined my PhD, I was asked to learn and use a different modeling technique and a different length scale which was not in the realm of my advisor's expertise. I work in continuum while she works in nano scale. Yes, the impact-factors vary in the journals for nano and continuum. But, all I am concerned with is the quality of my research work.

Post qualifiers and research proposal (my committee seemed happy with my theoretical knowledge, preliminary work and plans), I published one paper in a decent journal. But, my work was nowhere near that being done by my colleagues. I kept on working and completed three more manuscripts which are to be submitted soon. But still, my work is just mediocre and most likely will end up in average journals (IF &lt;2).

I feel that I should not have pursued PhD and I was not fit for producing good research. I also feel that I have screwed my chance of doing anything significant in academia. 

I also feel that I am still being funded and not fired because my advisor is a good person and is allowing me to stay regardless of my average performance out of pity.

Does my advisor owe me anything? Could it be that she keeps me only out of pity?
Having 4 papers published or submitted during a PhD period is actually quite substantial. Which journal they go to may be secondary, and there are many considerations. For example, at your stage of your career, getting anything accepted and published is more important than trying really hard to get that one paper into Science or Nature -- which entails a far greater risk of rejection and consequent delay, something one might be willing to accept as a well-known researcher in a field for whom one publication more or less makes no difference, but that you can ill afford.

But that's maybe not the question you're asking, so let me address that as well in the form of a story about myself: When I was a graduate student, I had always wanted to work at MIT or Stanford or a similar place, and to make breakthrough discoveries. Indeed, I know this to be true for many of my academic friends. But the longer I've been in academia (I've been a professor for 13 years now), the more I've come to realize two things:


By and large, science progresses not through discrete breakthroughs, but by continuously grinding problems down through the work of hundreds of people until the rare new ideas have been put into forms that can be used widely. Think about gravitational waves: yes, the follow from Einsteins equations and were theoretically well understood not long after, but then it took a hundred years until a whole community of hundreds or thousands of people had made the materials, detectors, and computational tools to actually use gravitational waves observable. All of these people made valuable contributions without which this would not have been possible, even though few of these contributions were published in the highest impact factor journals. What I'm trying to say here is that there is honor and value in doing good science, even if it never rises to the level of breakthroughs.
About breakthroughs to begin with: Of course, every grad student also wants to be the next Einstein. But few of us actually get to be. In fact, if you stay in a community, even if you're really really good, you will come to realize that there are people that are just so much better than you are. So not only do we not get to be the next Einstein, but almost all of us will actually never be at the top of our small sub-disciplines. But that doesn't mean that we're worthless -- there is honor in doing the everyday work moving science along and contributing to the scientific enterprise as a whole. Academia is composed of the high end of the ability scale, which is quite rarefied, and one has to learn to live with the fact that there are always people better than oneself. Take solace in the fact that the proportion of the general population who gets a PhD is already quite small, and you're in that fraction.