Virginia Tech’s Logan Thomas struggled with his passing game this season, but ESPN draft expert Mel Kiper, Jr., insists the redshirt junior remains a late first-round draft prospect based on talent alone. (John McDonnell/The Washington Post)

Virginia Tech play-caller and quarterbacks coach Mike O’Cain might be alone in this assessment, but he believes redshirt junior Logan Thomas was better than ever this year.

Though most simply see Thomas’s 14 interceptions and lower completion percentage as proof that the season didn’t go as planned, O’Cain “would’ve hated to go into games without him.” He marvels at how Thomas never seemed to crack mentally while running the Hokies’ pro-style offense and remained a “put-it-on-me kind of guy” through miscues that weren’t entirely his fault and losses that would have been worse had he not put his body on the line.

But even one of Thomas’s biggest fans can’t hide the obvious flaws.

“He just didn’t throw the ball at times with the confidence that he did the year before,” O’Cain said in a recent interview. “We talk about that comfort level and that just never really developed this season, for whatever reason.”

Thomas’s regression in his second year as starting quarterback has been a major story line throughout Virginia Tech’s worst season in 20 years. After being billed as a potential top-five NFL draft pick before the season, he has seen his stock drop in the eyes of scouts because of accuracy issues.

More importantly, though, his well-publicized backslide could lead Coach Frank Beamer to overhaul a much-scrutinized offensive staff after Friday’s Russell Athletic Bowl against Rutgers. But true to form, Thomas has defended his coaches in recent weeks.

“I’ve grown so much since just becoming a quarterback here in college, so I think they’ve done a great job getting me prepared and getting me ready,” Thomas said. “I mean, I was very raw when I got here, and now I’ve grown into, I guess, an NFL-type quarterback now, so I can’t hate on them. I can’t say they’re bad at all. I don’t know anything else but what I’ve got, and I think I’ve been just fine.”

It’s easy to forget Thomas came to Virginia Tech back in 2009 as a highly touted tight end prospect. This year was just his fifth season as a full-time signal-caller. But in 2011, he surpassed expectations when in his first year as a starter, established a school record for total offense while accounting for 30 touchdowns.

And in some ways, Thomas meant more to the Hokies this year than last. The 6-foot-6, 260-pound quarterback led the team in rushing with 528 yards, and is just 171 yards shy of breaking his own record for total offense.

But those numbers couldn’t hide the troubles Thomas had throwing the ball. His completion percentage fell from 59.8 percent to 52.6 percent and he had a tendency to overthrow receivers on short and intermediate routes. Thomas finished the regular season tied for the most interceptions among ACC quarterbacks.

Beamer believes the issues stem partly from a supporting cast that lacked experienced playmakers, but he was quick to point out Thomas “had some big moments” when he led go-ahead fourth-quarter touchdown drives against Georgia Tech, Cincinnati and Florida State.

Throughout his struggles, Thomas remained even-keeled publicly. But in weekly conversations with quarterback guru George Whitfield, he showed a more fragile side.

“I had to remind Logan . . . there’s a couple guys, and guys much more experienced than you, more veteran than you are, and quite frankly, in higher-powered offenses than you, that also had power outages every now and again,” said Whitfield, who has trained NFL quarterbacks Cam Newton, Andrew Luck and Ben Roethlisberger and worked with Thomas last spring. “I think that’s really the hidden beauty of this year. . . . Now he realizes just how pivotal his performance is.”

If Thomas were to forgo his senior season and declare for the 2013 NFL draft, he would have plenty of suitors. He graduated with a degree in human development last week and filed paperwork with the NFL draft advisory board earlier this month to assess his stock. ESPN draft expert Mel Kiper, Jr.,insists Thomas remains a late first-round draft prospect based on talent alone.

The looming decision has become a dilemma for Thomas, who has spoken with Beamer, O’Cain and offensive coordinator Bryan Stinespring about it since the regular season ended. He did note, however, that because of his consistency issues, “I don’t think I could go in and start an NFL game right now and be fine and come out with a win.”

“I believe he needs another year, and I think he believes that,” O’Cain added. “I don’t think there’s any question in his mind that another could help him. But at the same time, if he is projected or has a chance to be picked in the first round, well, if it was my son, I’m not sure how I would advise him.”