Yeah seems like a good choice. Setting the series on the third age would have been a pain with continuity, and just generally more limiting.
Setting things in the second age, there's less baggage, but you can still have Sauron but do him differently, and Rivendell, and use characters mentioned in the movies like Isildur, show Moria when it was still the great city of Khazad Dum...
You also don't need to fret as much about things looking or being different to what it was like in the movies. It's literally a different age.
Oh, and you can now have lots of different rings to make a big deal about instead of just the one
