The 49ers almost certainly aren’t going to the playoffs, but are they going in the right direction?

That is the primary question entering the 2017 season, which comes on the heels of a three-year nightmare that included a 15-33 record, three fired head coaches and an axed general manager.

In other words, rookie head coach Kyle Shanahan and novice general manager John Lynch have some very small shoes to fill. They’ve earned high marks for the competence they’ve displayed while adding 50 players to their 90-man roster.

Now, on the horizon, with players reporting to training camp Thursday, comes the hard part: winning games — at least enough to suggest last season’s 2-14 embarrassment won’t be repeated any time soon.

The starting QB

Brian Hoyer’s nickname is evidently The Placeholder, given the widely held belief that he’s a one-year stopgap before someone with franchise-QB potential replaces him in 2018.

However, Hoyer’s sneaky-good recent numbers suggest the 31-year-old could surpass the modest expectations most have for his 2017 campaign. In the past two seasons, he has had 569 pass attempts, 25 touchdown passes, seven interceptions and a 93.7 passer rating. Perspective: Washington’s Kirk Cousins, his possible replacement next year, has 25 TDs, 11 INTs and a 98.0 rating in his past 569 attempts.

Hoyer, above, likely won’t be a big part of the 49ers’ plans in 2018, but a strong debut season at least could keep him in the conversation as a legitimate if-all-else-fails option.

Bowman’s status

Will NaVorro Bowman, an erstwhile first-team All-Pro, become a second-string linebacker?

That seemingly remote possibility exists after the 49ers invested heavily in two other inside linebackers — first-round pick Reuben Foster and free-agent Malcolm Smith ($11 million guaranteed in contract) — while denying a report that Bowman was placed on the trade block.

Both head coach Kyle Shanahan and general manager John Lynch have stated Bowman, who has had two major leg injuries since January 2014, will have to fight to keep his starting spot.

In May, Bowman, above, sounded unfazed by his new competition: “I won’t be on the sideline,” he said. “I’m going to tell you that now.”

The Baalke-era picks

After receiving a contract extension in December from the old regime, tight end Vance McDonald, above, could receive a pink slip from the new guard.

And he wouldn’t be alone: Several underwhelming draft picks from the Trent Baalke era have tenuous job security entering training camp.

The 49ers have retained 27 of the 31 Baalke picks that Lynch inherited, but defensive tackle Tank Carradine, linebacker Eli Harold and wide receiver Bruce Ellington are among the notable past selections on the roster bubble.

The poster boy for the group is McDonald, a 2013 second-round pick whom the 49ers attempted to trade during the draft.

Can Hyde stay No. 1?

After providing measured praise of Carlos Hyde, above, after their hirings, Shanahan and Lynch have provided the starter since 2015 with competition: They drafted Joe Williams, signed Tim Hightower, traded for Kapri Bibbs and brought in undrafted rookie Matt Breida.

The biggest threat to Hyde’s starting spot is Williams, a 5-foot-11, 205-pounder. Shanahan and running backs coach Bobby Turner lobbied hard for Williams, who was kicked off the team at Connecticut, briefly left the team at Utah, and eventually convinced Lynch to place him on the 49ers’ draft board and trade up for him in the fourth round.

Williams’ one-cut running style is viewed as a better fit in Shanahan’s outside-zone scheme. Hyde flourished at Ohio State and had a career-best 988 yards last season in a shotgun-based, zone-read scheme.

The No. 3 pick

For starters, defensive tackle Solomon Thomas, above, has to sign his contract: The No. 3 overall pick from Stanford is one of three first-rounders who remains unsigned.

Once that happens, Thomas can start playing catch-up. Thomas couldn’t participate in an offseason practice with veterans because he needed to wait for Stanford’s semester to end in mid-June. It’s a similar situation that unfolded last year with guard Joshua Garnett, Thomas’ college teammate, and it could have contributed to his uneven NFL debut.

Despite his missed time, Thomas, the 49ers’ highest selection since Alex Smith went No. 1 overall in 2005, figures to play plenty along a defensive line that will include two other recent first-round picks: Arik Armstead (2015) and DeForest Buckner (2016).

Eric Branch is an S.F. Chronicle staff writer. Email: ebranch@sfchronicle.com Twitter: @Eric_Branch