There are actually quite a few differences. Just a few examples:
1) Most troops march in formation and changing direction/formation costs movement.
2) A broken (fleeing) unit can cause nearby friendlies to break as well - makes the Leaders a bit more valuable
3) Magic is a lot more varied than Psychic powers in 40K and can, in some cases, change the battle's outcome quickly.
4) Takes a lot more models to field a decent army, but they tend to look more unified (and can be a bit more of a bore to paint if you need lots of foot troops)
There's more, but that's all I can think of immediately. I've got the 6th ed rules and have a Lizardman army I'm working on (as well as Empire and Orcs that come with the box, of course). I've played 3 or 4 times and its fun. Biggest problem is that we get rules confused between 40K and Fantasy. Some of them are so close that it seems like they could really do one ruleset and just offer codexes that were labeled 40K or Fantasy. Be a lot cheaper that way too.
If you haven't had a chance, give it a run or at least watch a game. It's not half-bad and I've actually found that it helps my 40K tactics a bit.