Why does LyX add a \usepackage[T1]{fontenc} by default in all its
documents? My experience suggests that it's what makes PDFs generated by
pdflatex ugly.
Note that this is not the font type T1 but the encoding scheme. T1 gives latin letters, T2 cyrillic letters etc.
When you have problems with PDF, use T1-fonts. It is described in this PDF-FAQ:
http://wiki.lyx.org/pmwiki.php/FAQ/PDF
How to set LyX so that it doesn't add that line in the LaTeX code?
You can change the encoding in this menu:
Edit -> Preferences -> Outputs -> LaTeX -> TeX encoding
