My main beef was the pile in method of combat. In all the games I played, eventually it just became one huge fight somewhere on the battlefield where the majority of models would battle things out. Skirmished units did create a level of tactical feel for the battles, but frequently the tactics came down to unit activation.
My other beef was the rolling to determine who went first EACH turn. Instead of something reasonably predictable (either AB, AB method or AB, BA method) a game could turn literally on single dice roll as early as after the first turn. That drove me nuts.
The magic system AoS used also left me wanting. As HE had an additional nuance with the need to use magic well to get the most out of our squishy elves.
Some of these echo my initial impressions as well, but that changed considerably since the start of the game. I would recommend the general's handbook and the scenarios. With more terrain, and the scenarios, the game's dynamic changes completely. The big scrum in the middle (or somewhere) can happen when there's no scenario to force you to split the troops and commit on several places. It happened to me as well, when I played with WFB logic.
The roll for initiative on the turns is an odd one. I didn't like it initially, but again, with the scenarios and terrain it becomes a tactical element. Just today I had a few moments were it offered an interesting role and benefit to the game. IE: Mystical terrain gave me re-rolls on the wound and my general was locked with a tarpit in combat... By letting my opponent go first, I knew for sure I would retain my re-rolls and had a chance of clearing the tarpit unit on his turn, so that I could be free and charge in mine. It really depends on the game and scenario.
I'd recommend playing a few small games with slightly more experienced players. It will help considerably in shaping the game in the right way.