The Y-meter is visually complex with all of its variations so when you look at a full page of articles, it is very messy looking. As you mention you would like to visualize the story points, and I think this is a good goal. The visual should add weight to an article while still enableing the eye so casually slide past articles. A simple light gray bar next to the story points under the title would do this well. Also, given the amount of explenation of how it works and the fact that there is a "key" at the bottom of the page is a clear indication that the Y-meter as designed isn't going to be intuitive and is not likely a good direction to go.
The white HACKERNEWS title is hard to read. The white color works well and lightens up the header. I see that NEWS is slightly more bold, but not enough to distinguish it from HACKER very well. Still, all caps for words of length 4 or more impairs readablility and in this case unnecessarily.
The header links in white and slightly smaller font-size, do look more readable, so that is nice. Getting rid of the vertical seperators was a good choice as it de-clutters the header.
Search bar at the top, thank you! The current location at the bottom is terrible and this would be a welcome addition.
I'm confused by the meter next to the username. This seems to behave differently than the Y-Meters next to the stories. I'm not sure where to go with that one. The current numerical value in parenthisis are not great as there is no label, so it would be worth exploring additional options there.
The comment numbers on the far right are very far away from the story title which makes it difficult to tell what number goes with what story. It is especially difficult with short story titles. Perhaps your intention is that as a user hovers over the story title, the line is highlighted? While highlighting assists with tabular data such as in spreadsheets, it doesn't work on touch devices and is typically used in conjunction with other horizontal means of deliniation.
While placing all of the story meta-data on a single line allows you to make the font larger, overall the readability suffers as a result. Consider alternatives where the meta-data is shown below the story title, but in a lighter font. As you did with the header links, simply removing the pipes | and adding a little space would increase readability.
The "more" text at the bottom is burried on the far left on the same line as the Y-Meter Key and there is no whitespace above or below it. Give it some room to breath. The current Hacker News more button doesn't look clickable, so that is one area that could certainly use improving.
As per the upvote arrows sticking out to the left of the header, it looks like a mistake. I'm sure the intention was to do that, however it comes across as mis-alignment.
Overall, keep it up. I enjoy seeing design alternatives as there are so many ways to design a good website that has its own unique style and branding.
Cheers, -d-