She wasn't beautiful, but she had big, gentle brown eyes and a lovely smile.
Literal
Beautiful-person [copula-ではありませんでした] [but-が] big gentle brown eyes [object-を] having, pretty smile [copula-でした].
A charming character description. ではありませんでしたが sets up a concession. The positive qualities (big gentle eyes, lovely smile) outweigh the lack of conventional beauty. かわいらしい means 'endearing, cute.'