First, that was a weird game. Since when do the officials go under the hood and come back to the field to report that the replay equipment doesn’t work? I’m not even sure I believe that story, but it doesn’t matter. The 49ers lost their third game of the season, and their air of near-invincibility has decreased to an air of pretty-goodness.

San Francisco now finds themselves tied with New Orleans at 10-3 for that No. 2 seed, but even with the 49ers’ Conference record tiebreaker (49ers are 8-2 against NFC opponents; Saints are 6-3), their grip on a first round bye is tenuous at best. The Saints head to Minnesota next week before home games against Atlanta and Carolina. Unless the Saints lose their first home game of the season in Week 16 or 17, or Joe Webb leads the Vikings to a miraculous upset next Sunday, they’re going to win out.

The 49ers looked like they were a near-lock to go 13-3 before Thanksgiving when they were 9-1, and now winning in Seattle seems like a tough enough hill to climb, let alone winning next Monday against the Pittsburgh Steelers.

So what happened? I’m still not even sure, but here’s what we noticed at Casa de Rent Control, otherwise known as our apartment. That’s where we watched this less-than-stellar game with friends and family while celebrating my buddy Sean’s birthday (today) and mine (in a few days).

Passing game = failing grade

– The 49ers’ offense isn’t ready for prime time. Scrap that — their passing offense isn’t ready for prime time, mid-day or early in the morning.

– I would have to get my Singletary on and watch the film to know for sure, but I have a hard time remember an Alex Smith completion that traveled 10 yards or more downfield (in the air).

– Did the 49ers give Braylon Edwards a playbook this season? It’s hard to tell which is slower, Edwards’ routes or his thought process while “running” said routes.

– You know how when people watch the Saints or Packers and marvel at how many weapons they have to throw to? The Niners looked like the opposite of that in Arizona. Their weapons through the air included Michael Crabtree, Kyle Williams and not much else, and Crabtree and Williams were like weapons with silencers attached.

– Smith had several problems this game:

  1. He was sacked 5 times and hurried/hit on several other occasions.
  2. Again and again, Smith either has passes knocked down at the line or scrimmage or his throwing motion’s altered by oncoming pass rushers.
  3. Avoiding interceptions is great, as long as you muster at least 5 yards per pass attempt (Smith averaged 4.7 Y/A on Sunday).

Red zone trauma

– According to Team Rankings, the 49ers are now the worst team in the NFL at scoring touchdowns after reaching the red zone.

– It’s a strange problem for the team, since Jim Harbaugh and his staff are thought to be an infinitely more creative group than their predecessors on the offensive side, and the Niners have two above average receiving tight ends that should give Smith some targets to work with.

– But every time they get in 1st-and-goal range, it seems to go like this: they throw it to one side of the end zone to a wide receiver’s back shoulder on first down, then call a running play that goes nowhere before throwing a fade to the other side of the end zone from where they threw it on first down. Where are the tight ends when the 49ers get close to paydirt?

– We’re at the point now where it isn’t a joke to complain about stuff like Ted Ginn returning a punt to the 4-yard-line or Dashon Goldson (who made a huge error trying to fight Larry Fitzgerald for a “three flies up” kind of pass, which is Fitzgerald’s specialty) taking an interception to the 16. C’mon guys, you’re our only hope! Take it to the house! It’s not funny because it’s true…

Credit where it’s due

– Just to get this out of the way, even though the 49ers suffered through some strange officiating decisions and the defense missed a few tackles without Patrick Willis, the Cardinals’ defense has become pretty, pretty, pretty good.

What’s going on with Gore? 

– Only 10 carries, even though he gained 72 yards (going over 1,000 for the year) and ran for a 37-yard touchdown. Tim Kawakami tweeted something even scarier than 3rd-and-goal for the 49ers after the game:

(Small caveat: I’ve seen Gore limp off the field after practice, so maybe he limps around like that whenever he doesn’t have the rock in his hands.)

Defending the defense and special teams

– Sure, John Skelton showed off a side of his game Niners fans haven’t seen before (in disbelief, I started calling him “Productive” John Skelton during the second half), and indeed he threw for 282 yards and 3 touchdowns. However…

– The 49ers held the Cardinals to 3-of-14 on third down conversions (which only looked somewhat reasonable because the Niners’ offense went 3-for-17).

– The Cardinals gained 2.4 yards per carry.

– Aldon Smith sacked Skelton once, and almost had him a second time. He also showed off his patented “non-celebration celebration,” so you’d have to call this game a success when it comes to the Defensive Rookie of the Year race … except Von Miller had a sack against the Bears in a game way more people watched.

– The 49ers forced 3 turnovers.

– Ted Ginn was great on returns and the 49ers’ coverage teams were downright amazing against Patrick Peterson, who in his rookie season looks like a bigger Devin Hester. Andy Lee’s net average on 7 punts: 46.9 yards per punt. Wow.

In all, the 49ers’ template (win the turnover and field position battles) worked out rather nicely, and until a strange sequence of plays (the negated fake FG, David Akers’ miss, then a quick TD pass to Early Doucet) it looked like the 49ers were on their way to another Akers-led victory. One could either look at this game as a harbinger of doom (the Saints are coming; the Niners can’t score touchdowns or protect Smith) or a necessary wakeup call.

This game gives the 49ers no excuses, because playing without stars like Patrick Willis is part of the deal in the NFL. They didn’t have a short week, a long flight or a mighty team on the other sideline. The Cardinals are clearly on the way up (winning five of their last six), but after knocking out Kevin Kolb on the Cardinals’ first series this game was set up on a tee. There’s still a lot of work to do — and now part of the fun of this shockingly satisfying season will be in seeing how the 49ers rebound from their first bad loss.