It is actually fairly simple to lane vs. Annie as Darius. AAs are her only safe harass. Her Q and W both just barely outrange your Q. Take the block+unyielding masteries, and a Doran's Shield. That cancels out a lot of her AA damage, removing her safe harass.
Annie can only stun every 4 spells. and if she holds onto her stun, she can only farm with AAs (which is kinda hard when she has no AD and has a very slow AA animation.) So, if she wants to sit on her stun, shove the wave with Q, watch as she loses farm under tower. If she uses her spells to farm, wait until after she uses her passive proc, then go aggressive. You had MS quints and ghost, so you could easily close the gap to pull range. Annie pretty-much HAS to blow flash if you pull when she doesn't have stun ready, and ghost has a shorter CD than flash. Even if she flashed, if you got your W off, you could probably chase her down. Annie never built any HP even, she was so very killable.
Hexdrinker would probably been a better buy than Hydra, and mercs better than Ninja-tabi. The mercs not only had MR, but would reduce the stun duration.