Hmmm, my initial leaning would be spark plugs, but that's a lot of work just to check without a stronger indication.
But, here's my thinking. 2006 with only 3k miles sounds it spent a lot of its life sitting around, which if not properly prepped for storage is not great on spark plugs. Condensation from atmospheric moisture and left over water vapor from combustion can corrode spark plugs over time. Also the spark plugs can be damaged by freeze thaw cycles due to climate if there's water vapor. If the bike only sat for a short time before restart, it would have still been relatively hot. Electrical resistance increases with temperature, especially through insulative materials, which metallic oxides usually are. If the spark is losing amperage through resistance in the electrode surfaces, it may not be energetic enough to ignite until a couple cycles. Now, when I said the engine was relatively hot, that depends on what you're looking at, in terms of ignition enthalpy, that's a little cold; but for electrical resistance, that's still pretty hot. So the ignition energy threshold, what the spark has to give it, is higher than when running, but each no-start cycle increases the cylinder enthalpy through the spark heating the plug and the compression heating piston and cylinder, until the spark can push the reaction over that edge. On a cold start, resistance in the spark plugs is lower, and so the spark is more energetic, quick start.