poor font quality when exporting to pdf

It appears that the problem is that your LyX and LaTeX installation is using bitmap fonts instead of vector fonts for text. Try setting the default roman font for the document to Latin Modern Roman in the document settings.

Document > Settings > Fonts > Roman > Latin Modern Roman

I had this problem, too; when I removed this:

\usepackage[T1]{fontenc}

the problem disappears and the fonts become very nice and sharp again!

Maybe you are using fontenc, or maybe it's some other package that's causing the problem. Check this possibility.