The last two games have been a coming-down-to-earth process for the San Francisco 49ers, learning that Colin Kaepernick isn’t a quarterback who can handle anything thrown at him or a lacking receiving crew, while the team itself isn’t as intimidating, strong and ready for another Super Bowl challenge as some might thought they were.

Even in the win against the Green Bay Packers, a 34-28 performance that had Colin Kaepernick get crowned as one of the elite quarterbacks in the NFL thanks to his 412 yards, 3 touchdowns performance, cracks were shown. Not by Kaepernick, but a defense that’s no longer as good against the run, especially in the redzone, as in the past, and a running game, be it through Kaepernick or Frank Gore, that is going to struggle compared to last season, when the 49ers ranked third in the NFL with 5.1 yards per carry, and 4th in total yards on the ground.

The defense, which ranked third last season in total yards (294.4) and second in points allowed (17.1) has given up at least 27 points in each of it three games this season, ranking only 13th in total yards against and 25th in point allowed with 28 per game. Over the last nine games, including the last postseason, the Packers have won only five games, allowing 29.1 points per game and losing by 20 or more three times, including twice on their visits to Seattle.

Having Aldon Smith leave the team indefinitely until he deals with his inner demons isn’t going to help, but actually letting him play so soon after his arrest might not have been the best of ideas from Jim Harbaugh, who is looking more and more helpless than angry over the last couple of weeks.

If losing to the Seattle Seahawks and getting bullied from the first minute wasn’t such a surprise considering who the Seahawks are and the result of that game last year, having the Colts come to San Francisco and be just as dominant, presenting an excellent running game (179 yards) and a defense that had no problem getting to Kaepernick or containing him (3 sacks, one fumble, one interception) was somewhat of an image shattering moment for the 49ers and for those expecting big things from them.

Kaepernick over the last couple of games has been the biggest disappointment. His numbers against the Seahawks and Colts? Completing only 26-of-55 (47.3%) for 277 yards, with 0 touchdowns and four interceptions. Running? He did rush for 107 yards on 16 carries, but it was more about his inability to find open receivers than actually designed running plays the opposing defenses couldn’t stop.

Having only Anquan Boldin (Vernon Davis is out too) to throw to is a huge problem considering Michael Crabtree is out for quite a while and Mario Manningham isn’t coming back soon as well. However, Davis did play against the Seahawks, and it wasn’t very helpful anyway.

Kaepernick is a good quarterback, but not a great one, yet (and maybe never), that makes even the least impressive bunch of receivers look like they can go for 100 yards each game. He seeks safe options and isn’t very good when it comes to adapting to new targets. He is only in his actual second season in the NFL, but those who declared him as the next great quarterback need a bit more patience. His inability to complete throws for longer than 10 yards downfield against the Colts (1-of-6) and in general (2-of-13 in the last two games) is just another problem he now has to try and fix.

The 49ers are still a very strong team, but one that relied too much on what worked last season, not realizing teams pick up on things quicker than they might have thought. Not it’s on Harbaugh, who has never lost two games in a row as an NFL head coach, to find a way to make Kaepernick efficient again, and the 49ers to look like a formidable opponents, before it actually becomes too late to turn things around.

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