Perhaps none of the issues was as glaring as the inability to get the ball downfield.
Gabbert completed just two passes all season that traveled at least 21 yards downfield and his 37.3 rating on deep throws was second worst among all quarterbacks, according to Sportradar.
He badly missed open receivers on deep passes numerous times, including a key interception two weeks ago against Dallas and being wildly off-target on deep throws to Rod Streater and Torrey Smith in last week's loss to Arizona.
With the Niners providing little threat deep, defenses have been able to crowd the line, which has hindered San Francisco's running game and limited opportunities for big runs after the catch.
Deep throws were a big part of Kelly's offense in his three years in Philadelphia when the Eagles were tied for fifth in the NFL with 69 completions on those passes and ranked second in touchdowns with 26, according to Sportradar.
Kaepernick, with his strong arm, had more success on those throws even as he struggled in other aspects last season when he lost his starting job to Gabbert midway through the year. He completed 10 of 26 deep passes for 451 yards, three touchdowns and two interceptions.
The Niners (1-4) hope Kaepernick can hit some of those throws this week against Buffalo when he makes his first start since Nov. 1, 2015.
''I think there's just small things here and there that we need to clean up, we need to correct as a whole,'' he said. ''Hopefully those are things that we progress on this week and it shows Sunday and helps us get a win.''
Before Kaepernick could do that, he signed a restructured two-year contract Wednesday. The new deal replaces the previous deal that ran through 2020, takes the Niners off the hook for a $14.5 million injury guarantee for 2017 and gives Kaepernick the right to void the second year and become a free agent in March.
The contract also converts Kaepernick's $2 million roster bonuses this year into guarantees and he can earn an additional $1 million based on meeting certain playing time thresholds, a person familiar with the deal said on condition of anonymity because details were not made public.
ESPN, which first reported the contract, said the Niners will not be able to use the franchise tag on Kaepernick if he opts for free agency.
This is the second time Kaepernick has taken over as starter in San Francisco midway through a season. In 2012, he replaced a concussed Alex Smith and led San Francisco to the Super Bowl where the 49ers lost 34-31 to Baltimore.
With his breakaway speed and cannon arm, Kaepernick looked like the poster child for the new breed of NFL quarterbacks. He led the Niners to road playoff wins in Green Bay and Carolina after the 2013 season before his late interception in the end zone ended a comeback attempt in the NFC title game in Seattle.
He took a step back the following year and then plummeted last year when he threw for only six touchdowns and had five interceptions in eight starts before losing his job.
The hiring of Kelly with his spread offense that favors running quarterbacks was thought to be the tonic to revive Kaepernick's career but his offseason was limited by operations on his non-throwing shoulder, right thumb and left knee.
A tired arm shut him down for two weeks in training camp and Kelly went with Gabbert as starter, saying Kaepernick had not regained the strength he lost after surgery and wasn't ready to be starter again.
''He physically is not where he was pre-injury,'' Kelly said. ''Before that he was a little bit bigger, a little bit faster, a little bit stronger. He will admit that. He's worked as hard as anybody I've been around in terms of his rehab.''
But with Gabbert ranking as one of the worst quarterbacks in the league, Kelly decided Tuesday it was time for a change.
The Niners rank last in the NFL in yards per play (4.5) and are tied for the most three-and-outs with 21.
''I think we need to improve in all areas of offensive football,'' offensive coordinator Curtis Modkins said. ''I don't think that's a single one defining deal. We made a change because we felt like this gives us the best chance to win on Sunday and moving forward, so that's why the change was made.''
NOTES: CB Jimmie Ward (quadriceps) missed practice. ... Among the players who were limited were G Zane Beadles (ankle), LB Ahmad Brooks (groin), DT DeForest Buckner (foot), DT Quinton Dial (knee), DT Glenn Dorsey (knee), WR Jeremy Kerley (ankle), TE Vance McDonald (hip) and S Jaquiski Tartt (quadriceps).
AP NFL website: www.pro32.ap.org and www.twitter.com/AP-NFL