Markakis should have a great year and Pedroia sorta "broke out" last year. I dont think he can put up the same numbers this year and he already has an oblique injury. I have Pedroia on my team and dont have another second basemen...but The Riots always out there. What is your lineup?
I think we've already seen Pedroia's best season, and I'd prefer Markakis, but I'd bet that Pedroia's got a little more trade value.
If you think that Mark would be on your team for the long haul and you'd be happy with that (A very reasonable position), just take the RF.
If it's a very active league, I'd try taking and trading Pedroia while he's creeping into 2nd rounds in redrafts (i.e., before a game is played).
Full disclosure: I bump Markakis down if the OF isn't separated into RF, CF, and LF. If it's not separated, I'd have to say take the 2B. The trade value would be just too much higher to pass up.
Markakis.... pedroia is overrated, he can polish his "mvp trophy" all he wants... take jose lopez in the 9th round and you'll get more production than Pedroia, at least value wise