After the Navy game, I attempted to collect my thoughts about the Weis era. What went wrong? I dunno. But if I had to give an opinion, and as I am an anonymous poster on the internet, I do, here is my speculation:
Weis arrived with supreme confidence in his schematic ability. He inherited a team with some performance issues, but that did have some basic core competencies. His players could do enough various things that Weis's play calling flair led to a significant improvement in offensive performance. Weis saw this and unfortunately drew two mistaken conclusions. The first was that he believed that his emphasis on scheme was vindicated, and he did not alter this view in light of the harbingers of USC and Ohio State 2005, and Michigan 2006.
The second was that he erroneously assumed that his play-clling prowess could compensate for other short-comings on his team, with the absolutely fatal assumption that he could work around an inability to control the line of scrimmage on both sides of the ball by out-thinking defensive coordinators. Despite ominous warnings that this wasn't going to work, Weis made his next collossal blunder: he decided to coach around his teams weaknesses by putting more emphasis on personnel packages, eccentric play-calling and odd gambles. This led to a snowball effect that was magnified by limited practice time, and had other detrimental effects as well.
(Speculation here) I suspect that Weis opted to use his limited practice time to force-feed a metastasizing playbook that was increasingly directed toward papering over poor execution, poor fundamentals, and lack of diverse competencies. As a result, the deficiencies that started to show themselves in 2006 became more neglected and our fundamentals got worse, we became less competent at more and more areas of the game. What Weis had to work with to compensate for these shortcomings became more and more limited, until our offense atrophied into a fading (pun intended) caricature of a college offense. The result was Syracuse, 2008.
But Weis made matters worse still. He redoubled his focus on his play card, even though it by now consisted mostly of plays we could not run. As a result, he lost track of games, and his game-management, which started out acceptable, became abyssmal. Poor clock management, momentum-killing play sequences, and most tellingly, a virtual concession of the field position battle ensued. As our competencies dwindled, opposing teams could take away those things that Weis was counting on as the substrate for his schematic genius, making our offense degenerate into hapless lobs, and desperate heaves.
The nail in the coffin though, was what bugged many fans as lack of intensity, or lack of motivation, but what was in reality lack of focus. Weis's emphasis on scheme at the expense of fundamentals, execution and field discipline manifested itself increasingly as confusion, stupid penalties, missed assignments, and poor execution. (Again, just my opinion here:) Focus comes from presenting players with a very limited number of contingencies in any given situation. As an example, middle school quarterbacks should have to contend with no more than one decision; "do this or this," high school quarterbacks two or three options, (this, this or this) and college quarterbacks, three or four. Pros can deal with contingencies as time permits. If you allow too many contingencies, the player's focus is devoted more to decision making, often leading to indecision, and less toward performance. The result is a player who appears poorly prepared, and poorly motivated, and a team that sucks. The receiver zigs when the quareterback thinks he'll zag, the safety lets the tight end run free thinking the linebacker has him, the right tackle blocks no one because he can't process the decion tree in the face of a novel blitz. The tell here is that the natural tendency of coaches is redouble their efforts at addressing contingencies, thinking that the actual cause of the deficiency is the cure for it, and the team gets worse as the season goes along: November fade.
Lots of new coaches make similar mistakes, so why did Weis flame out? Because one attribute that every great coach must have is that he must be a good diagnostician. Weis apparently is not one himself, and either did not surround himself with any, or created an environment where he wouldn't access their expertise. When the wheels started to wobble, Weis couldn't identify what was wrong; he began grab-bagging, flailing and morphing into Gerry Faust.
So, in summary: Weis reasonably tried to emphasize what initially was his strength, which he could get away with becaue his team had some base competencies. He did not recognize the warning signs that this would not work long-term. He thought he could compensate for an inabliity to control the line of scrimmage with clever play-calling (which will be the cause of death noted on the Weis tenure's death certificate), he did not feel comfortable trading off scheme development for player development and establishing competencies beyond "Above-average or great quarterback to above average or great receiver." He became a progessively worse gameday coach as he focused on his dwindling options as a play-caller, and he failed to realize that his failure to develop skills that he apparently took for granted completely negated any advantage his play-calling abilities may have provided. His emphasis on areas other than player performance allowed poor tackling, mental mistakes, poor blocking, and 6-4 with a team that once had BCS aspirations.