Really, there's not much to criticize.
However, it's inevitable that some of the players they passed on will end up being great pros for other teams.
And that's where regret can come in.
As the following five players have productive careers, the 49ers' draft decision-makers may be kicking themselves for not pulling the trigger on them.
I had no issue with the 49ers addressing their biggest need with their first-round pick. Eric Reid should be quality safety for many years. He might have been the best option in the whole draft for San Francisco to try to win a Super Bowl next year.
However, the 49ers' long-term cornerback outlook is awfully cloudy. Tarell Brown is scheduled to be a free agent after the 2013 season. Carlos Rogers was a sieve in coverage last year. The Niners could enter next offseason with only Chris Culliver penciled in at cornerback.
Desmond Trufant was my second-favorite cornerback in the draft behind Alabama's Dee Milliner. The former Washington Huskies star has the size and athleticism to shut down top-tier receivers.
To make matters worse, the Atlanta Falcons took him. It wouldn't surprise me if Trufant is making plays all over the field against the 49ers in the playoffs for years to come. If so, 49ers fans may ask, "Why didn't we draft that guy?"
But the 49ers already took a safety in the first round?
Although this is true, taking Reid didn't shore up the safety position for the long run. Donte Whitner is scheduled to be a free agent after the 2013 season, and he was already the weak link in pass coverage in 2012.
D.J. Swearinger is a ferocious hitter with an ideal body for a strong safety. He may not be blazing fast, but I'd guess that his 4.67 40-yard dash time is comfortably faster than Whitner's (he's clearly lost a step since being drafted in 2006).
I have no issue with the Niners taking Vance McDonald, who should make a big difference next year as San Francisco's No. 2 tight end.
But down the road, the Niners may wish they took the former South Carolina star to pair with Reid.
Some draft analysts believed the Niners would consider Jesse Williams with their first-round pick. Well, they ended up passing him up six times.
He would've been incredible value with their last two picks of the fourth round. Of course, the Niners drafted two studs in Quinton Patton and Marcus Lattimore with those picks.
Clearly, by passing on Williams and all the other quality nose tackles in the first four rounds, Trent Baalke and Jim Harbaugh are confident in Glenn Dorsey and Ian Williams manning the nose tackle position next year. Still, it must have hurt a bit when Seattle drafted the former Alabama star early in the fifth round.
Williams could instantly help Seattle slow down Frank Gore and the San Francisco running game.
I'm not too high on Jordan Poyer's open-field tackling and overall athleticism. However, you're not going to find a cornerback with his instincts and skills in the seventh round of most drafts.
Poyer would have been a great value pick in the sixth round. He had a monster senior season at Oregon State with 14 passes defensed, seven interceptions and five tackles for loss.
Sure, sixth-round pick Nick Moody could be an outstanding special teams player. But he may never see the field on defense, whereas Poyer could have worked his way into some nickel packages.
Expect Poyer to be a productive nickel corner in his rookie season for the Philadelphia Eagles.
Regret is an awfully strong word for this slide. After all, Matt Scott went undrafted, and the 49ers obviously have their quarterback of the future in Colin Kaepernick.
Still, instead of taking B.J. Daniels, the Niners could have spent one of their three seventh-round picks on the former Arizona Wildcats quarterback.
OK, OK, Jim Harbaugh is a quarterback guru who clearly knows more about the position than, say, I do.
Now that that's out of the way, I just don't get why Scott wasn't drafted. Sure, he's incredibly raw, but I saw some big-time potential in his one year as a starter for the Wildcats.
Plus, he's athletic enough to be a threat in the zone-read offense.
Don't be surprised if Scott ends up starting for the Jacksonville Jaguars down the road.