2.0 - 3.0 are very marginal gains, so yes it is still worth it. Games and GPU's do not fully utilized 3.0 technology yet. At least not until more demanding games come.
1x 680 > 460sli so yes it is going to be better. It will also limit any microstutter if you use a 3 monitor setup. If your on 1980x1080p your graphics will be top of the line pretty much anything on ultra.
If it is worth it is your call. Is the extra cost worth the performance upgrade? 2x 460's are giving you pretty good performance if you bought for around $300. However, plan on tacking $200 more for a 680. So its up to you if you can afford it. Imo it is worth it. You might save on the power bill some to. ha
Originally, I bought them for $400 around a year ago and planning on using around $350 along with the money I'm getting from selling these, which is around $210, to buy a GTX 680. And, I do plan on using a three monitor setup after I buy this card (5760x1080), so I suppose it would be worth the upgrade, especially since you said 3.0 isn't really being utilized yet and the difference between 2.0 and 3.0 is small.