These are both different classes of cars. I shifted from Wagon R to Swift so can fairly comment on these aspects.
Fuel Average
With my driving style, I used to get 16.5 -14.5kmpl without AC while 14.5 - 12.5kmpl with AC on a mix of petrol and high octane in Wagon R, while since I shifted to Swift it's been 11 -12.5kmpl with AC on High Octane only. Bearing in mind I don't do long journeys usually a daily two way 27km (each way) commute from pindi to isb. Result on motorways may vary. Definitely with the 328cc difference in engine and traction the consumption is way higher on Swift.
Parts Price:
For a new car this isn't a concern. Aside from specialised part, most routine maintenance is comparable. A little hike on Swift is there but then again since it's a 9 year old model, part availability isn't a question.
Easy Maintenance:
Maintenance within cities isn't a problem or in town where suzuki dealerships are there. However routine maintenance is easy on both cars.
Long Route Drive:
I took the wagon R to Kalam and it went there without a problem. Driving was more comfortable and so was the ground clearance. However the back seat was stiff for long journeys. With the low clearance of Swift I am still to grasp the confidence to take it to off road places. I feel the comfort is low, as shocks are stiff. It's still better in the front, but leg room in the back seats is too less in a swift while the seat itself being more comfortable.
For all means wagon r to my experience is a more practical car for in city use. While the swift a gass guzzler is perhaps better for long journeys. Please also bear in mind that a Swift has far expensive tokens particularly if u register in Punjab and you must bear in mind those expenses. If given a chance I'd buy the wagon r again. But my only problem with wagon r is its poor braking and poor traction due to narrower and small tyres. It is also uglier than the swift which seems more balanced. But the choice really depends on where you use it and what for.