Lots of possibilities: contaminated fuel, blocked fuel injection nozzle or fuel filter, fouled spark plug(s), clogged air filter, loose exhaust hose (especially if this is FX HO model).
What to try: New fuel (higher octane). Look at the air filter (should be clean and dry.....no oil), try running it without the air filter. Carefully check exhaust hose (there is a noted problem with defective hoses and clamps in 06-08 FX HOs, and a loose exhaust hose could cause this problem (dealer will replace for free the defective hoses and clamps). Replace spark plugs (plugs are very common cause for poor performance in skis). Could even be something else (electrical, etc.), but these are the more common problems.