OK, it looks like iTunes can clear up my confusion, lol.
They are selling 25 episodes of season one, including the two hour pilot and the three hour season finale. (Exodus, Part One was one hour long, and Exodus, Part Two was two hours--weird.)
They are selling 24 episodes of season two (including the two hour finale), and 23 episodes of season three (again including the two hour finale).
My confusion stems from the fact that sometimes the episode guides refer to a two hour show as one episode, and sometimes as two (with a part one and part two). So however you count up the number of episodes, if you go by actual broadcast hours you get 25, 24 and 23.
I hope that when they agreed on 16 episodes per season for the last three years, that included a two hour finale each year (giving us 17 hours total per season). I'll take every hour I can get...