Let's talk about the weaknesses, we need to start by the Footwork Joe's footwork tends to tighten once he's engaged with his hands on his opponent. While the fact that he often keeps his legs active is a positive point, it must be noted that they can sometimes stop on certain reps. Alt can still improve in this aspect, but it's really the tightening of his foot base that concerns me, as when he does this, he's no longer in a position of strength and can therefore be easily thrown off balance. 

Alt also tends to play too high. Granted, he stands at 6'7", so I understand it's challenging for him to get lower than Rushers at 6'5" or less, and who themselves strive to play low. However, the fact remains that he straightens up too often and too quickly once the block is engaged, which prevents him from playing with sufficient power angles. He'll need to work on this, but if he can improve in this area, he could become truly formidable.

The two previous points lead us directly to another important aspect in assessing Joe Alt, which is his inability to dominate in running situations. He really struggles to create movement on running plays, and it's clearly not his strong suit.
Of course, arriving too high and with a tight foot base makes his Run block approach imprecise, and it's not uncommon to see him miss a block at the second level because of this. Similarly, always on his Run blockOn running plays, he tends to arrive with his weight forward (or leaning forward, if you prefer) to maintain the push that will help him create movement. However, the problem is that as a result, he is no longer under control, and a simple Speed move can allow the LB to get rid of him.
Still on his Run block and being off-balance forward, when he blocks in running situations, he has a strong tendency to extend his arms, somewhat like a defensive lineman. As a result, he puts himself off-balance forward and often ends up on the ground after his running blocks, having lost his balance. It is imperative to work on these points to see Joe progress.

As we've seen in his strengths, Joe Alt has a good ability to consistently reposition his hands, but that's also because his initial hand placement is often quite mediocre. This naturally goes hand in hand with the fact that Joe plays too high, but his hands are often positioned quite high on his opponent, which doesn't help him effectively engage the player he needs to block without making it immediately apparent. Even without intentionally trying to make Holding on the sly, Joe's hands are simply far too high; he consistently touches the facemask of defensive linemen, which is a penalty that's often called in the NFL, much more so than in college football. Alt will absolutely need to work on this aspect. 

In terms of IQ and game vision, Joe will clearly need to progress with the help of NFL coaching. During the Notre Dame vs. NC State game on a passing play where Alt was supposed to stay in man-to-man protection on his EDGE, Joe followed the EDGE for 5-6 yards of depth even though he was dropping into zone coverage (which is a penalty, by the way; an offensive lineman cannot move more than 5 yards downfield on a passing play), and this completely threw off the offensive line, resulting in a sack. Alt is sometimes caught out by this kind of Stunt and I find it unfortunate considering how technically dominant he can be on Pass pro.
Later in the same game, during an outside running play on the opposite side that required him to pull, once again Joe misread the play and decided to block a player who was already engaged in a block, which not only disrupted the running back's read but also allowed the defender, who had already been blocked before Joe intervened, to shed the block and make the tackle. It's a shame because if Joe had made a good read and had gone straight to the second level, there was only one linebacker to block, and it would have been a gain of over 10 yards guaranteed for his running back. I think here again, Alt could make significant progress and really improve his overall level. 

Joe sorely lacks power in my opinion and seems to have really based his game on finesse and technique. However, if he decides to truly base his game on technique, he will need to make much more effort to improve on the technical details mentioned above in order to be dominant at the pro level.
Still on this lack of power and dominance, I find that Joe doesn't use his punch enough; we hardly ever see him punch on his strikes, neither on Pass pro, nor his Run blockHe does use his hands, which also seem to be rather quick in placing them on his opponent. However, he doesn't punch. It's a real shame considering the nice reach he has; with a quick and snappy punch, he could be even more unstoppable than he already is in Pass pro and could delay the defensive lineman in order to engage him low on running plays, which could greatly help Alt to be more dominant in running situations, which is precisely one of the areas where he needs to improve.