This problem is probably due to the MathematicaMono font which is introduced in v10.
Defining the problem:
Some fonts ("[","_","]","=", etc.) are rendered badly with strange thinning in v10 in some notebook magnifications.
This is obvious when you compare the renderings from v10 with those from v9.
Analyzing the problem:
I found that all of these ugly-looking fonts were rendered in MathematicaMono font (specifically, MathematicaMono-Bold.ttf font in this example) by using the method described in my comment for the question section. MathematicaMono fonts are new in v10: we only have fonts named Mathematica1Mono, Mathematica2Mono, and so on, up to v9. These results suggested that the problem is caused by the new MathematicaMono fonts.
Next, to test this hypothesis, I substituted the MathematicaMono-Bold.ttf by Mathematica1mb.ttf (which contains Mathematica1Mono-Bold font) copied from my v9 installation folder. I renamed the name property of Mathematica1mb.ttf by using FontForge program ("Mathematica1Mono-Bold" to "MathematicaMono-Bold") and installed in the v10 font folder as MathematicaMono-Bold.ttf.
After the substitution, the notebook was rendered as in v9 at least for characters like "_" and "=":
Sadly, "[" and "]" were not fixed because Mathematica1Mono font lacks glyph for these characters. But anyway, the substitution experiment partially confirmed my hypothesis.
What's wrong in MathematicaMono font?:
I have no answer yet. So I can not provide the complete solution. But I found a strange thing in MathematicaMono font. In all of the newly introduced MathematicaXXX.ttf fonts in v10, "Win Ascent" and "Win Descent" properties for OpenType fonts are in strangely big values (5000 and 3500) compared with the values in v9 Mathematica fonts (1747 and 479). This makes the previews of MathematicaXXX fonts small in a strange way when you open the fonts in Windows font viewer program. But, I could not fixed the original problem even when I edited "Win Ascent" and "Win Descent" values of MathematicaMono-Bold font in FontForge.
I hope my answer helps someone to solve this problem.
I found a clear evidence that the problem is in the MathematicaMono fonts.
After you "install" the MathematicaMono.ttf and MathematicaMono-Bold.ttf, you can use MathematicaMono fonts in softwere other than Mathematica. Here is the MathematicaMono fonts rendered in Microsoft Word:
The rendering problems reported in Mathematica were completely reproduced in MS Word! This indicates that the problem is not in the Mathematica Front-end but in the font itself.