Well, I do agree that the draft is an area of OOTP which could use quite a bit of improvement.
The draft does seem a bit too top heavy. Running a draft with even five rounds results in too much busywork dealing with prospects whose chances of success are extremely low. These are problems.
I would like to point out, however, that any one for one comparison of 1st round picks in reality vs. OOTP is going to be a waste of time. The real baseball draft has 50 rounds. The draft in a game like OOTP is always going to have fewer rounds, because the logistics of dealing with a farm system that large and that involved wouldn't be fun for more than a few zealots. So if you're running a 5 round draft, you might want to think of that first round as being roughly equivalent to the first TEN rounds of the real draft.
Somehow, I'm guessing that every major league team is going to have quite a bunch of players who were selected in the first 10 rounds.
-Spielman