I play both versions as well. 2010 has so much more interesting features than 40d and searching for good embark site is less pain in the butt, one reason being the guaranteed magma. In 40d, to find site with flux, iron ore AND magma is very tedious and irritating process, and usually there is about 0-5 such locations in single map, depending on how big embark size you use.
On the other hand, you don't have to worry about hitting caverns in middle of your bedroom area in 40d. But then again you have less floor to use in 40d, I think the norm is 15 levels bellow the ground.
Setting up early farms is much easier in 40d, as no irrigation is needed. At times muddying in 2010 gets to my nerves, as I have to carefully plan where I put my farms, take in to account the water sources while embarking and so on. No such hassle in 40d.
40d has less bugs, especially when considering nobility. All the nobles work as meant, so you can actually get that Dungeon Master.
2010 introduces hospitals, which WILL safe your soldiers from certain deaths (well, certain death in 40d) most of the time, though due bugs it's not promised.
The military went big overhaul, in 40d it's much faster to make more or less working military, but on the other hand in 2010 the military is much more efficient. And no unneeded deaths from sparring anymore. Also, equipment handling is better in 2010 as soon as you learn to use it. In 40d organizing equipment to squads meant forbidding/dropping/locking combinations to get the military wear the equipment you wanted, and still it was not guaranteed. In 2010 you can assign the squad to have steel equipment, and they will go and get steel equipment most of the time. Again due bugs they may mess up with their equipment, like not removing old equipment and so on. Also no more kills with just wrestling in 2010, which I think is good thing.
So, to summarize, I play both versions, depending on my mood and what I want from my fortress.