I've ordered from EE about 20-30 times and have never had any big issues with them. Their prices are pretty good for online ordering, though I typically wait until I have a coupon or some kind of discount before turning to them. I wouldn't hesitate to order from them again though and now's a good time with the current discounts.
Sorry to hear that you had a bad experience. If the item isn't in stock, then I'd rather have them be honest about not knowing if/when new supply would come in. A lot of online places would just tell you it's on the way, then maybe never deliver (I'm looking at you TRU). And if it said "In Stock" when you ordered, maybe it was just one of those rare times where they didn't have it flagged correctly on the site. That's definitely not the norm as I've never run into it before. I'm sure if they did have it, they'd do whatever they could to get it to you and collect their money.