You have a valid point bbasebrawl, but there is a problem when the prospect draft is allowed to include the current year MLB draftees. This has come up in each of the leagues I'm in at one point or another (in GMKL current year MLB draftees are off limits) and the general consensus has been this:
Because all current year MLB draft picks can sign contracts any time from draft day to the start of the college school year (think Scott Boras here) it often happens that half the 1st round picks sign and half wait until the end.
Because there is no fixed date for any prospect draft in any league, we don't know who will be signed when the draft begins. Or who signs while the draft is in progress for that matter.
So in order to be fair it's been a pretty universal decision to lay off this years MLB draftees because of the whole "signing" issue and let them add to the next years drafts. There are always guys that think otherwise in each league, but the majority usually think this is a fair process.