In my opinion PECOTA can work really well but you have to make sure the values are adjusted well. The default 180 batters to 80 pitchers can still favor pitchers, especially in middle rounds. That's because there are no 1st and 2nd round worthy pitchers besides Santana and maybe a few others. Also, the reason I think why it felt like it went against intuition is because it values some types of players way more than we're used to, and that's sometimes a good thing because we're reminded to find players that can contribute to multiple stats, not always just one.
Here's my team that I drafted using PECOTA.
http://www.fantasybaseballcafe.com/foru ... p?t=257404
Both of us have a few big bats, a great pitching staff, and a bunch of fillers for the rest of the O spots. Not very impressive batters overall.
My solution is to continue using PECOTA in your next draft, but bring along a list of Average Draft Positions so you know who you can wait on and who you should take right away. That should help solve your problem.