For $2,000 I would look into an SV650. You'll find them in decent condition, albeit high mileage, at that price.
For $3,000-$3,500, you can find them with lower mileage (I've seen some really clean ones, around 8k miles) and not ragged out or dropped.
Commuting on the highway is something I thought about doing on the ninja, but not just yet...and only on Saturday mornings, when there is no traffic at 5:30am