There was some issues with the es system in the early years, then again in 04. If you're looking at a new one, no problems have been reported since then. As long as your realize that if you use it in severe conditions, the maintenance requirements are increased.
The ES system costs about $200 more than the manual version, but with the es you get a speed/odometer, gear indicator, and hour meter, well worth the difference. The es system is great for those without a lot of atv experience.
Wife had a Recon Es, and I have a Rancher Es, and highly recommend them.