Depreciation and other costs are par for the course. You don’t buy a large family car without a premium badge and expect it to hold its value for ever, but the significant proportion of Skoda owners who go in as private buyers means that residuals are better than some of the more fleet-focused, discount-territory alternatives.
Besides offering more kit and being easier to live with, it'll prove easier to sell on and potentially hold its value better.
All of the engines are frugal but, predictably, many buyers will make a beeline for diesel variants which will further help prop up the residual values of the models in question.
On paper, the SE L 1.6 TDI looks like a particularly good option with a sensible blend of kit and economy, if not the pace you might want. The lethargic acceleration, however, means you have to be a bit frisky with the throttle to make serious progress - and that has an impact on fuel economy.