I'll make quick numbers, that no one will read because it's all about Prius versus superbike in here...
F650GS, the thumper, 60mpg. Tire set, $140 for Kenda K761, very popular tire with the DS crowd. A tire set should last for 9,000 miles, lets say both are changed at the same time, and that the set is $200 installed.
Chain & sprocket, DID X-ring, $200, good for 20,000 miles.
About scheduled maintenance, sparkplugs, air filter, valve clearance and fork oil every 12,500 miles, engine oil and filter every 6,000 miles and fuel filter every 25,000 miles.
Will calculate for 25,000 miles.
3 x tire sets: $600
2 x chain: $400
2 x 2 sparkplugs: $12
2 x air filters: $33
2 x 1 qt BMW Fork oil: $15
6 x BMW oil change kit (oil, filter, etc) filters: $260
1 x BMW fuel filter $151.15
2 x valve adjustment $400 (or DIY, $2.50 each shim, assuming you change all, $20)
3 x OEM Brembo brake pad sets: $420
It takes regular fuel, and assuming a high-ish $3.60 per gallon and a mid 65mpg...
417 gallons required, at $3.60, that's $1502 in fuel.
Total costs for 25,000 miles: $3794 or $0.152 per mile. That's assuming a midly competent DIY that can do everything but adjust the valves.
Going with BMW dealership rates, 6K miles service is $320 including parts, 12K service is $550 including parts...
That would turn into:
3 x tire sets: $700
2 x chain: $500
3 x 6K services: $960
2 x 12K services: $1100
1 x BMW fuel filter $151.15
3 x OEM Brembo brake pad sets: $570
417 gallons required, at $3.60, that's $1502 in fuel.
Total costs for a non mechanical inclined rider 25,000 miles: $5483 or $0.22 per mile.
Start with a couple years old F650GS, which hold their value pretty well, and you'll have a hard time finding anything cheaper.
Edit: Forgot to throw a quart of engine oil, shop towels and a brush to lube up the chain.
Depreciation! According to KBB a 2009 G650GS with ABS is $5847, a 2007 G650GS with ABS is $5410... Lets assume an even steeper depreciation, 25,000 miles is like "OMG, it's going to blow up" miles, so it will start as a $5847 bike and 2 years and 25K miles later end as a $4410 bike...
That's an additional $0.06 per mile, bringing the total to $0.21 per mile for the average DIY and $0.28 for the bonehead, even counting depreciation it's beating the old Civic.