Hi Twee,
Can't give you a definative answer I'm afraid - there isn't one! They are both cracking cars. I'm assuming they are new?
My personal feeling would be to go for the Skoda.
I suspect that being a VAG group car the reliability will be better, depreciation will be less and in the longer term parts availability will be better (depends on how long you intend to keep it whether that makes a difference). There are more skoda/vw dealers around than Suzuki anyway.... (if I remember correctly the Fabia is just a tarted up Polo)