First about automatic transmission:
In India we usually do not have the modern automatic gearboxes[now only has the concept caught up but remember there is a premium for these and you will have to buy cars of higher segments like the NHC CVT].
Even the authorised dealers itself are not experts on these gearboxes so repairs and maintainance is a big problem in India.Another thing is that there is much lower resale value for the automatics.
Also the lower segment automatics are gas guzzlers and are not exactly what you would call fun to drive,so keep away from the wagonr/santro/esteem/zen automatics if an automatic is not absolutely needed.
Now this link from team-bhp market place is a good pointer for second hand cars rates[updated]:
http://www.jmdcars.com/marketpriceforallusedcars.asp
The swift and wagonr are from two different segments with the swift giving you a higher segment experience.Comparisons cant be made between the two but if its only about money then go for the wagonr,else the best gift for your dad would be the swift.
Ps: Are you going in for a used wagon/swift or a brand new one.