After the Eagles started the season 1-2, it was clear this team had pronounced weaknesses.
So they tried making some changes. Casey Matthews moved from the middle to the weak side. Then from the weak side to the bench, as Brian Rolle replaced him.
Kurt Coleman wasn't getting it done at safety so they instead went with Nate Allen.
Offensively, the coaches continued to work with Michael Vick and the offensive line to provide better protection and improve effectiveness against the blitz.
No one knew if those changes would solve any of the Eagles' problems, but what happened instead Sunday afternoon was that a whole new set of concerns was revealed.
Through three weeks, the 49ers had very much relied on a dink-and-dunk offense. Tight end Vernon Davis has proved to be a dangerous playmaker for Alex Smith, but that was about it. Entering Sunday's game, Smith was averaging 6.8 yards per attempt. That was actually better than his career average of 6.2 yards per attempt. No wide receiver had more than 80 receiving yards TOTAL in three weeks.
Meanwhile, Frank Gore was averaging just 2.5 yards per carry. His longest run of the season before today was for 16 yards. He had just three carries of 10 yards or more in three weeks. Oh, and he was nursing an injury.
So what happened? The Eagles allowed seven plays of 25 yards or more. Seven!
A 40-yard Gore run. And later a 25-yarder.. A 26-yard completion to Davis. Completions of 26 and 30 yards to wide receiver Joshua Morgan. A 44-yard catch and run by Kendall Hunter. And a 38-yard completion to Michael Crabtree.
The Crabtree completion might be the most troubling because it came against Eagles cornerback Nnamdi Asomugha. Asomugha's played four games, and in three of them, he has been beat for a big play of 25 yards or more. That's not even counting a 41-yard pass interference penalty in Week 1.
Some of that is on Juan Castillo for the way he's using Asomugha. But at some point, the player has to take responsibility.
Getting back to Castillo, he is going to take a lot of heat too, and rightfully so. This really has been the worst-cased scenario on defense. I'm not sure what this unit does well.
Consider this: Smith had a QB rating of 143.1 against the blitz going into today. Did you notice that the Eagles sent seven at Smith on the Morgan 30-yard touchdown? Castillo makes that call.
Smith's 112.1 QB rating was the fourth-highest of his career. Last week, Eli Manning set a career high with a 145.7 QB rating against the Eagles. Wasn't pass defense supposed to be this team's strength? I sure thought so. They are just getting picked apart by opposing quarterbacks. That's 10 touchdown passes allowed in the last three weeks.
The run woes continued too. Gore averaged 8.5 yards per carry, the fourth-highest average of his career in games where he ran the ball at least 10 times.
In the fourth quarter of the last three losses, the Eagles have been outscored 36-0. They've allowed five touchdown drives. And we're not talking cheap drives either. On average, teams have had to go 68.6 yards. The 49ers went 2-for-3 in the red zone. Opponents have now scored touchdowns on 8 of 10 red-zone trips against the Eagles. That 80 percent rate is worse than last year's historically bad unit coached by Sean McDermott.
Offensively, new issues emerged. The team turned the ball over in the red zone for the third consecutive week. They turned it over a total of three times for the third straight week. Tough to win when you give the ball away like that.
Michael Vick and the offense managed just three points in the second half in a game where it felt like they could have easily scored 40 and put the game away. I am usually not one to go overboard with the whole run/pass ratio, but considering that Vick had suffered a concussion and hand injury in back-to-back weeks, perhaps it wasn't the wisest move to run play-action fake after play-action fake. In the end, Vick dropped back to pass 54 times.
LeSean McCoy, meanwhile, who had been the bright spot on this team through three weeks, got just nine carries.
And finally, special teams. Going with a rookie kicker and a rookie punter were huge concerns entering the season, but Alex Henery looked good in the first three weeks, hitting all four attempts from less than 50 yards.
Against the Niners, with David Akers on the other sideline, Henery missed attempts from 39 and 33 yards. Suddenly, the kicking game has vaulted to near the top on the list of concerns.
If you're looking for a bright spot, we're only a quarter of the way through the season. The Giants and Redskins are both 3-1, but the Eagles face New York once more and Washington twice. The Cowboys also blew a 20-3 lead and are at 2-2 after a loss to the Lions.
Maybe Castillo will figure out how to use his personnel better. Maybe Asomugha will become the shutdown corner he was in Oakland. Maybe the offense will take care of the football and turn those just-misses into big plays. And maybe Henery will regain his confidence and kick well.
But those are a lot of maybes as this team prepares for a pair of road games before the bye week.
In case you missed them, I provided instant observations on many of these topics right after the game.