On the field, this is still an excellent team. The defense is weaker than last year without Smith, Macdonald, Bowman, and Dorsey and with three new starters in the secondary, but they can roll in Tank Carradine and Ian Williams on the DL without much drop off (Williams actually was the starter ahead of Dorsey last season before breaking his leg, and Carradine was a potential all-pro talent coming out of college before tearing his ACL). Even without Bowman and Smith they still have a bunch of pro bowl-level players on defense (Justin Smith, Patrick Willis, Ahmad Brooks, Eric Reid), and if they can hold the fort until November when Smith and Bowman return they will be very tough in the playoffs.
The offense will have to be better to pick up the slack, and it should be much improved from last year. The WR core has been massively upgraded. Last year they started the year with Kyle Williams and Jon Baldwin as the #2 and #3 receivers: those two combined for 15 receptions and both were cut by midseason, and FB Bruce Miller finished 3rd on the team in receptions with 25. This year, they have a healthy Crabtree, Boldin returns after a monster season, they added Stevie Johnson from Buffalo to play in the slot and signed Brandon Lloyd as a deep threat (he was supposed to be training camp fodder but had a great camp and surprisingly made the team), plus they drafted Bruce Ellington, who will probably return punts. Vernon Davis is still one of the best tight ends in the league. They may actually use 3WR sets this season, which their personnel didn't really allow them do for most of last year.
At RB, despite losing Kendall Hunter for the season they have the ageless Gore with LaMichael James as the speedy change of pace guy, and they drafted Carlos Hyde to be the power/short yardage back, plus they could add Marcus Lattimore by midseason. FB Bruce Miller is one of the best blocking fullbacks around (a dying art). The OL has a new center (Daniel Kilgore, promoted from backup) but everyone else is back (Boone finally signed last week after holding out) and reasonably healthy to start the year, and while they weren't as good in 2013 as in 2012 it's still one of the better lines around.
So the weapons are there, for the first time in a long time. This is the best offense on paper the 49ers have had since Steve Young was throwing to Jerry Rice and Terrell Owens, and the first time in many years defenses won't consistently stack the box and dare the 49ers to throw. In order to get back to 11-12 wins Kaepernick will have to take another step forward. I think he will make significant progress this season, not to MVP-level but I think he'll be a comfortably Top-10 QB.
The schedule is hard with the AFC West, but with Arizona and St Louis's off-season injuries it doesn't look quite as rough as it did in May. They don't have to play Seattle until Thanksgiving, so they can hope to have Smith and Bowman back for those matchups. And they have managed to keep one of the league's best coaching staffs mostly intact.
So that's the on-field stuff. Obviously the off-field stuff is a big issue, what with the Harbaugh/Baalke power struggles and all the arrests and suspensions. If any team is equipped to handle that stuff, though, it's the 49ers, who have one of the tighter locker rooms in the league and lots of strong, veteran personalities who will keep the team focused (Justin Smith, Patrick Willis, Frank Gore, Vernon Davis are the main leaders). They've had major in-season "distractions" the last two years (in 2012 it was the QB controversy, last season it was Smith's DUI arrest) and mostly emerged unscathed. Harbaugh will no doubt do the whole siege mentality/us against the world thing.
Without Smith and Bowman for 2/3 of the season, I don't think they have enough to catch Seattle, but I'd be very surprised if they miss the playoffs. 10 wins and a wild card seems like the most likely projection. There's some downside risk: say, the new secondary can't cover anyone, without Smith there's no pass rush, Kaepernick struggles, Frank Gore finally hits the wall, Harbaugh and Baalke openly feud all season, and they go 7-9 and miss the playoffs, but unless Kaepernick gets hurt and we are subjected to the Blaine Gabbert experience, I don't really see it. There's just too much talent up and down the roster here.
