@divesh_code – I think that’s a great question.
I personally would prefer to only have the node size be based on the amount of incoming links and nothing else. Just like Google used to rank the quality/authority of pages: By how many other pages link to it.
Ideally, and to your point: This ranking should be a preference to choose from along word-count and others.
At the moment, node size is determined by the amount of outgoing and incoming links to a note. To understand it better I created a dummy project and see how the graph changes. Here’s what I’ve learned:
Vault state 1:
I created three files:
- The “Index Note With Outbound Links” (center) renders as the largest node in the graph. I personally would prefer this node to remain as small as all the others.
- The “Index Note Without Outbound Links” (bottom right) with the exact same word-count renders small.
- The “Authority Note” (bottom left) has no inbound links yet and remains small.
Vault state 2
I added a link to the “Authority Note” from all other notes.
- The “Authority Note” now renders larger – Just the way I want it. Yay!
I looked into the code and from what I gather, it’s that for each link between two nodes, BOTH nodes receive an increase in weight while I would prefer only the “linked-to” received that +1. The weight property is then used in the getSize() method which I believe to determine the rendering size. I might be completely wrong though in my assumptions!
Anyways, I’m super excited for the upcoming graph filtering and hope we can all configure it the way we each want it to 
Edit: Formatting and added getSize() screenshot for illustration.