One of the main questions will be the future of the offense. Although Tyler Thigpen was a bit less impressive at the end of the season, he's presumably earned a shot at the starting job next year. If the Chiefs intend to continue using the spread sets they installed this year, they could draft Tim Tebow after the first round to provide some competition to Thigpen. If Tebow didn't pan out as a quarterback, he could probably be turned into an effective slot receiver, a la Matt Jones.
A quick aside regarding the terminology used to describe the Chiefs' offense this year, since local sports talking heads seem to have an especially difficult time describing it consistently, using terms like spread, shotgun, and pistol interchangably: a spread offense can be run out of any formation that has no more than 2 RB/TE combined. The spread involves 3, 4, or 5 WR that are "spread" across the line of scrimmage from sideline to sideline (although WR bunch sets will occasionally be used, usually to run a WR screen). The shotgun merely means that the quarterback does not take the snap under center, but rather from a position usually about 5 yards behind the center, although some offenses will have the QB a yard or two deeper or a yard or two closer to the center. One such offense is the pistol offense, which originated at the University of Nevada a few years back. In the pistol, the QB lines up about 3 yards behind the center, and the running back lines up directly behind the quarterback, giving the appearance of an I formation. The purpose of the pistol is to provide more of a power, straight-ahead running game than can be used out of a normal shotgun formation, in which the running back is positioned at the side of the QB and most running plays begin side-to-side rather than straight ahead.
Thus, spread offense principles can be used in a single-back formation with the QB under center, or a shotgun formation, or even, more rarely, a double back formation with no TE. Conversely, a shotgun offense and the pistol offense are not synonymous with a spread offense, although they can be run as such.
When the Chiefs modified the offense for Thigpen in the middle of the season, they began with some shotgun spread and fairly quickly moved to pistol spread formations, which made sense with Larry Johnson as the running back, as the pistol's straight-ahead running game complements his skill set.
However, in the last few games the Chiefs moved away from the pistol back to basic shotgun spread, with the QB lined up deeper and the RB lined up beside him. Unsurprisingly, this negated Johnson's straight-ahead ability, and his effectiveness declined sharply. Time and again, he was caught for a loss running side-to-side out of the shotgun.
Some have questioned whether the spread formations employed by the Chiefs can be successful in the long term in the NFL. While NFL defenses will continue to improve against the formations, there is no question in our mind that the formations can meet with continued success as long as they are being run by players who are proficient in the systems. NFL defenses are built around size and speed, and spread principles help to negate both; witness the neutralization of Miami's usually-effective speed rush at the end of the season.
One key for the Chiefs will be what type of running back they use next year. It seems doubtful that the perpetually-discontented Larry Johnson will return, perhaps leaving Jamal Charles as the starter. Charles is more suited to the side-to-side running style needed to run out of the regular shotgun formation. However, if Johnson or a similar back is named the starter, the Chiefs should consider returning to the pistol formation.
Of course, the new GM and possible new head coach may very well decide to draft a traditional pro-style quarterback and install him into a traditional system as they continue to rebuild these team, leaving the question of the long-term efficacy of shotgun spread offenses in the NFL to be determined at a later date by a different team.