That is a long time to store the bike. Normally for short term storage I would just trickle the battery for a day every month or two and drain the carb. For storage in the years category I would do this (just me though, might be overkill)
1. Drain tank and carb of all fuel. Mist tank with oil if possible to prevent rusting.
2. Remove battery and plan on replacing it when I took it out of storage.
3. Flush front and rear brake system and replace with new clean fluid.
4. Oil and filter change before storing.
5. Put a few tablespoons of oil in cylinder and turn the engine over a few times so it doesn't rust (seize) while sitting.
6. Lubricate all cables.
7. Lube the chain heavily.
8. Get the bike off of the tires if possible to prevent flat spots.
9. Clean and lubricate all control pivots (levers etc.)
10. Cover the bike and try to keep it in a dry area. Direct sunlight will check plastics and tires, so covered in a garage would be best.
11. Flush and replace coolant with fresh stuff.
I think that would cover it in a dry environment, maybe a little overkill but when you come back to the bike a few years later hopefully you would be able to throw a new battery in it, flush the tank with some clean fuel, check tire pressures and it would hopefully fire up and not give you any problems. The reason I mentioned flushing the brakes and putting clean fluid in the system is any moisture in the system could cause your calipers to seize up... A real PITA
If your in a humid salty environment you might have to look at coating bare metal surfaces with something to keep them from rusting while it's sitting. If you really wanted to go nuts you could probably put dielectric grease in all the connectors to prevent corrosion while it's sitting. Bikes (all machines really) don't really like extended storage so anything you can do to prevent problems when pulling it back out into the light of day would be well worth it I think.
Again, this might be overkill, but this is how I would store it if I knew I wouldn't be getting back to it for two or three years. Hopefully people who have stored bikes for years will chime in with their experiences as I've never stored one for more than 6-8 months.