I think someone above nailed one difference truly. 40K feels much more cinematic. It is much more up close and personal. Fast paced, shrapnel flying. How many will make it through the barrage?
Warfare is bloody and 40k makes it really bloody. How many men will you have left? That is sort of what is in the mind of many commanders. I belive 40K catches the feel of ugly and brutal war much better than Fantasy.
The movement rules in Fantasy also makes the game more abstract. It feels like a large scale wargame, lumbering formations moving and turning, the combat have become abstracted to increase speed of play etc... Still, GW have droped any mentioning of a scale in the game and many say it is a One to One relationship, which makes it utter BS!
A small unit of formed men WILL change formation much faster than a large one and the unit commander will know instantly when his unit is ready for next command.
The larger the formation, the longer the formation change, the longer the order for wheeling will take to make it through etc...
If GW treated WHFB like a scaled game, with say one mini representing 10 soldiers or something, and adapted the game accordingly, it would make more sense and be more cohesive.
40K basically works on a One to One basis, and since it uses the dynamics of modern warfare with loose firing lines, assumes soldiers will usually make the most of cover and such, the game works much more fluently.
Also, even if we say the movements are simplified to unit types, things gets more uncertain because when some special rules for terrain kicks in. How long will my men move? Will the get past that wall or will the squad end up straddling it? If I run I might make it into the cover and claim the objective, but what if I donīt and get stranded before the barrels of that Heavy bolter squad?
And even when you got units that can fleet, like Eldars. What if I donīt make it into contact and end my charge a few inches before that line of Tau pulse rifles
Lots of things to consider and I feel it is not dissimilar from the modern combat enviorment. And tactical desicions ainīt simpler today than before, when you marched in formation. They are simply different. For those who enjoy the mathematical side of gaming, I guess Warhammer is more pleasing. Makes you feel in control and such. Make you feel like a general. Truth is that you have too much control of everything in WHFB, compared to what a general in the days of yore really had.