I take Hughes too but I think it may be closer than you say.

those 4 reasons are spot-on, and add a few more:

-the Yanks are in the best position to judge and they clearly rank Joba above Hughes.

-people obsess about minor Joba injuries, but it's Hughes who has been injured much more -- have to worry about that.

-there are worries about Hughes' ability to keep his stuff late into the games. Joba has shown the ability to keep his stuff into the 7th/8th innings (some people below wonder about that, and clearly they haven't' ever watched Joba pitch in the minors).

it's frankly cut and dry. just because hughes was teh better prospect coming into last year doesn't mean he is now. just as Homer Bailey's star has dimmed a bit, so has Hughes'.

I know I am playing devil's advocate but hey why not. Hughes is two years younger then the rest except for Gallardo and H. Bailey.  As a 21 year old, he has done a lot live up to the name of "phenom"

FB--before his lost 2007 season, Hughes had a 92-93 fastball that topped out at 96, 97 without great control. He topped out at 94 in the bigs last season was consistently 90-92. Some of the 89-91s you saw in September, when healthy, were two-seamers, so no, its not flat. Plus pitch.

CRV--Hughes's curve is arguably his best pitch. It's not loopy--in fact, it has a hard downard break. It is in the low-to-mid 70s, and it causes many swings and misses--a strikeout pitch. Plus pitch.

CHG--Hughes's change is a work in progress. It is average, but it really isn't ready to be considered a set-up pitch. The changeup, as is, is there just to give the hitter a different look, but it should improve through spring training and the regular season.

SLD--Hughes's slider isn't talked about much. Hughes used to throw a nice slider, but, as usual with many Nardi Contreras prospects, it was scrapped in favor of a curveball. He throws it in bullpens, but not much in games. It has good movement, and it is in the 80-83 MPH range--however, it sometimes moves too horizontally. This is a result of not having a great feel for the pitch anymore, as he didn't throw it much last season. He should throw it more often, IMO, as it looks to be an above-average pitch.

Control/Command--Hughes's control is his trademark. When right, Hughes has great control and could likely hit a 1-inch box if challenged--plus control. He also has plus command, but it didn't show last year because he left the ball up due to his leg problems.

There's your Phil Hughes scouting report. Sounds like an ace to me...

almost every scouting report I read stated that when healthy his fast ball sat 92-95 touching 96 and upper 80s with his 2 seamer.  Also his curveball is a true power breaking ball that sits in the low 80s and is a strikeout pitch.  I have watched almost every game he has pitched because and most of his strikeouts came from his curveball.

Oh and his slider is just as nasty, which used to be is plus plus pitch in highschool.

Now the reason why he sat in the low 90s was because of his hamstring and ankle injury ... he tried to be too careful not to re-injure it.  

Once he gains back his confidence with his front leg he will be able to kick it up a notch on his FB.

Fully healthy and with his pitching coach to keep his mechanics right all of next season, things look good for Hughes.