Don’t go for the 1.6TDI if the car will be used for town/urban most days. The 1.6TDI (as do all diesels now) has a Diesel Particulate Filter <DPF>. If the car is not doing, on average, 50 plus miles per day, the chances are that the DPF will clog up (as it’s not doing the miles which trigger a cleaning process to burn off the soot). This will end up costing you LOTS of cash and problems (and you’ll also find anything relating to DPF’s is not covered by warranty).
There’s also an on-going issue with the 1.2 and 1.4 engines – there are some which use a chain for timing (as opposed to a belt), and the chains are jumping teeth in use, hence knocking out the engine timing. There was also an issue with cylinders cracking on the TSI engines.
So usual catalogue of VW issues! However, Skoda warranty and customer care is the best of lot, out of the VAG group.