Something else to bear in mind regarding company car tax.
If you choose a petrol engine, the BIK tax will go up by 2% every year.
If you choose a diesel engine, the BIK tax will go down 1% next year, then up 2% each year thereafter.
In the case of my suggestion above, assuming you're a 20% tax payer, the Skoda (with no additional options) will cost you:
2015/16: £606.00 (£50.50 / month) (17% BIK)
2016/17: £677.07 (£56.42 / month) (19% BIK)
2017/18: £748.34 (£62.36 / month) (21% BIK)
2018/19: £819.61 (£68.30 / month) (23% BIK)
Another consideration with the small engine, is that you'll get paid the lowest mileage rate, currently £0.11 / mile for a <1400cc petrol. If you go diesel, <1600cc is only £0.09 / mile!
The Mazda 3, with the 2L petrol engine (1998cc) will get mileage paid at £0.13 / mile. Real world fuel economy shouldn't be wildly different between the Skoda & the Mazda, according to the official figures. Company car tax for the Mazda is a little higher than the Skoda (it's in the next bracket up).