All of these guys have top 10 talent, but where they rank on year end lists will come down to how talent evaluators view these injuries and other fractors which change some profiles.
Adam Morgan - It was a bit of a lost season for Morgan. Actually, it was more than that. Morgan went down in May with "a small tear" in his rotator cuff. Before the season Morgan was seen as a sure #3/4 Starter. In April he pitched to his potential with a 3.23 ERA and modest K numbers, countered by a low BB ratio. A mid-rotation starter is valuable and had Morgan kept performing as he did the first month, he'd be an easy rank, no lower than the 7-8 range. The problem is UCL means Tommy John and while TJ is not 100% guaranteed to return a Pitcher to their prior norm, it does in most cases. Rotator Cuff, is not so clean. Shoulder injuries, in many cases, are career killers or force guy to the 'pen to limit wear and tear of 150+ innings a season. I'm not an orthopedic surgeon, my degree is in Sales and Marketing, so I don't know how big of a problem a small tear in the rotator cuff is. That makes Morgan tough for me to rank, as I don't know quite what he is right now. The project manager in me says "assume the worst and develop a contingency plan as though he'll never hold up as a Starter" (the Phillies are clearly mitigating the problem by limiting his innings from July on this year), the Prospect watcher says "It's not wise to ding the guy for an injury that you don't know enough about." In the end I think I need to lean closer to the second option, with a touch of option 1.
Tommy Joseph - I feel bad starting off with 2 of the Org's top 5 prospects before the season, but there are significant questions about ToJo going forward. To his benefit, he has good power potential, he's a solid defensive Catcher and Pitchers have raved about his game calling and everyone raves about his leadership. He doesn't take many walks, he's never hit for a particularly good average to offset that patience and he's always sported a highish K rate. Still, all of that was true last year and all of that would keep him a Top 10 prospect this year. However, Tommy Joseph has had significant concussion issues and it seems his latest, which cause him to miss most of the season was form simply being hit in the mask by a pitch, I don't mean to downplay the impact of that, I've had my bell rung that way and it's not fun, but as a catcher, that will happen several times a season and if you can't absorb that blow without injury, you can't really stay behind the plate. The Phillies essentially mentioned that was a possibility a month ago in an interview with Joe Jordan. As a strong defensive Catcher with decent power Joseph is a pretty good prospect, as that profile would make him an average starting Catcher. His only likely move would be to First, where his profile would be pretty bad. Essentially, he goes from a top 10 prospect to Org. filler. The hope would have to be that he spends a few seasons focusing solely on hitting with the distraction of Catching removed and his power explodes and his hitting improves by leaps and bounds. I really don't know what to do with Tommy Joseph, but I have little faith he remains behind the plate. This could be a tough call.
Jesse Biddle - Biddle's top 5 on this list, not two ways about that. However, he pitched from May through the end of the season with whooping cough.I have had whooping cough, it's damned miserable. Your chest and back muscles end up sore from the coughing and wheezing for breath and you feel quite tired most of the day, as it can be tough to get a good night's sleep and sometimes all that coughing and wheezing just wears you down. I can't imagine playing a pro sport while dealing with it, and I certainly can't imagine not sucking very badly while doing so. None of that has to do with ranking though, since we have no idea what he could have done, if healthy. He wasn't and that's part of his record. Honestly though, I do have to consider it as a factor. Essentially, if I'm looking at two players as being pretty equal, but one played the year with an illness or injury and the other didn't, that may sway me towards the one who, with injury/illness impacting him, was still able to perform at a high level.
Roman "Candle" Quinn - I'm not sure quite what to do with Quinn. He essentially lost the season to an injury, but when he went down for the year, he had almost exactly the same sample size as 2012. He didn't really improve in any area (many more HR, but fewer XBH overall, more steals, but with a worse - though still excellent - success rate), but he didn't really regress anywhere except BA, which is mostly explained by a 60 point drop in BABiP. I see 2013 as a hold steady year, when he really needed improvement in his fielding, or really his throwing. The good news is that reports state Quinn gets to the balls, he just muffs the throws from time to time. That's not uncommon for a guy learning the position and it's one of the more fixable problems. A move to Center may well be in his future, but if I were the Phillies I'd give him, at least, one more year at Short to see if he can right the ship. With the bat, Quinn needs some work, but his walk rate is respectable and his bat should get him hitting soemwhere in the .250-.260 range with an OBP around .350 and an OPS in, perhaps the .750 range. That's not bad at Shortstop. The question here is whether holding steady allows him to hold steady on rankings or if he slides (and I don't mean he doesn't move at all by holding steady on the list, JP Crawford's glove immediately ranks him ahead of Quinn right now, in my book, I mean does he slide further than that).
Maikel Franco - A month ago with 2 weeks left in the season, Franco, in my book, was no worse than #2. Then the Phillies threw a confusing monkey wrench in things by moving Franco to First for the last few weeks of the season. What the hell? Look, if they did that as a hedge against a Ryan Howard injury in 2014, so Franco can play, then that's fine. Here's the thing though, Franco's bat may profile as top 10-15 among Third Basemen, but at First, he'd more likely be bottom half of the league to perhaps even bottom third. That's a big change to his profile. He's #1 or 2 on my list if he's a Third Baseman, a move to First probably pushed him to the back half of the Top 10. If the Phillies just want to get him some experience at First, but the long term plan keeps him at the hot corner, he's a top prospect. But, what if they've come to realize he won't work at Third after watching Michael Young spend a year bothing grounders? What if the move to First is a realization that Franco can't play Third in the Majors?