It is almost a given that the Cubs will get someone to overpay for Shark if indeed this comes to fruition. Playoff teams become desperate, and even though prospects are highly touted, there is never a guarantee. That is the difference between Shark and some prospects.
The pitching prospect(s) that the Cubs do receive could be an ace, blow out his arm, be a middle of the rotation pitcher, back-end pitcher, reliever, or a bust. There is a lot that can go wrong with a prospect, but it's rare for things to go just right.
I would argue that top 100 ratings don't really do a good job in reflecting what pitchers are. I think fangraphs or bleedcubbieblue covered this recently in that a top 25 hitter and a top 25 pitcher aren't equivalent in value. In fact, hitters tend to be more valuable which is slightly counter intuitive because they are more projectable where as pitching even at the top levels is iffy. For pitcher it's more a case of which players have the best raw tools instead of who is the best "pitcher."
As for what the cubs will get you're right it's not a guarantee. But if we go back to say 2008 to allow for time to develop and take a 3 year look at the top 25 baseball america pitchers you get these guys
2008
3. Joba Chamberlain, rhp, Yankees
4. Clay Buchholz, rhp, Red Sox
7. Clayton Kershaw, lhp, Dodgers
8. Franklin Morales, lhp, Rockies
10. David Price, lhp, Rays
15. Jake McGee, lhp, Rays
17. Wade Davis, rhp, Rays
21. Rick Porcello, rhp, Tigers
24. Nick Adenhart, rhp, Angels
2007
1. Daisuke Matsuzaka, rhp, Red Sox
4. Phil Hughes, rhp, Yankees
5. Homer Bailey, rhp, Reds
10. Andrew Miller, lhp, Tigers
11. Tim Lincecum, rhp, Giants
16. Yovani Gallardo, rhp, Brewers
20. Mike Pelfrey, rhp, Mets
21. Matt Garza, rhp, Twins
23. Adam Miller, rhp, Indians
2006
6. Francisco Liriano, lhp, Twins
7. Chad Billingsley, rhp, Dodgers
8. Justin Verlander, rhp, Tigers
10. Matt Cain, rhp, Giants
22. Jon Lester, lhp, Red Sox
24. Bobby Jenks, rhp, White Sox
So, you have Bucholtz, Kershaw, Price, Lincecum, Garza, Verlander, Lester, Bailey and Cain as "front line starter." Joba, Jenks, McGee, Andrew Miller and Morales ended up bulllpen arms. Gallardo, Liriano, Porcello and Billingsley have been some where between front line and middle of the rotation. Pelfrey, Hughes, Matsuzaka and Wade Davis were back of the rotation guys. The only total busts were Adam Miller, and Adenhart.
Granted it's a bit of a small sample size here but 9/24 were 1/2 starters(38%), 5 were relievers(21%), 4 were in between(17%), 4 were back of the rotation/fringe starters(17%) and 2 were out right busts(8%). As such, I'm not sure if I'd use the word rare with regard to things going right as over this period if you got a top 25 guy you had a 50/50 shot of getting a guy similar to Shark(or better) and 38% shot at a front line guy.
That being said, this sort of shows to make the trade even halfway worth while the cubs need to get back at least a top 25 prospect and probably 2 top 100 players.