The magic system in 3rd Ed Fantasy Rules! is much, much more streamlined than 2nd ed, the magic pools are more fluid, the spells are tweaked too.
Aside from that, there's very few changes in the actual mechanisms. There are LOT more army options and lists available, a few changes and new units (Rifles, cavalry has been tweaked, etc). Lots of cleanups and tweaks from 2nd.
The cleaned up magic system alone is worth it, along with the tweaked units and army lists.
Unfortunately I play FR!3 about twice a year with an old friend, everyone else locally has forgotten about 15mm fantasy, which is a shame.
The other shame is that his very-slowly-growing Undead army (which has been growing by about one base every year for the last ten...) nearly always beats my beloved Dwarves, my mob-o-Orcs and even my high-chivalric Human Knights. Damn necromancers, anyway. (oh wait, they already are... never mind, then...)
We did have one supremely satisfying battle last year in which my Dwarven army, glutted with artillery, manged on the first three turns to destroy all four characters in his Undead army. Freakish lucky to-hit rolls for me, awful bad luck in character-survival rolls for him. His entire force was undead, no living allies of any sort, so when his last character caught a mortar round with his forehead the entire army evaporated like mist. My Dwarves shrugged and ordered the ale casks opened. Strangest battle we'd either had in years of FR! play!