The fuse is there to protect the charging circuit from overload, say if the battery becomes shorted or too much load is placed on the ignition coil (the ignition coil is the alternator) while the smaller fuse may work well when the battery is fully charged, you may find it will blow if the battery is somewhat discharged and pulling higher amps on a recharge rate.
As to it not starting on idle, generally I start any of my 2 strokes on full throttle and never had an issue, the starter motor does turn the engine slower than the starter rope, that may be a compounding factor.
