Initial thoughts: It feels a bit disjointed, but I’m not sure why… It has complex layers, which I like (Veteran’s proud shell cracks from doubt (question his life), rescue mission, betrayal, stakes of the mission raised, etc.), but they are laid out separately instead of tying back together like they probably do in your story. I’m going to break down your hook and write my train of thoughts. Maybe that’ll help you see what an editor might be thinking.

“Disciplined and without regret, Captain Janner Kohl exemplifies the professional soldier. When the commander of his mercenary guild orders him to rescue the kidnapped son of an old flame from pirates, Janner wonders if he really has lived without regret–at least in regard to his feelings for her.” – This tells us how others see him, yes, but how does he see himself? Maybe mention his soldier’s pride here. Then when he questions his life without regret, it has more meaning than just a philosophical exercise.

“And the raw recruits he’s forced to train for the mission test his patience and push his self-control to its limits.” – This feels tacked on. Actually, is it needed here in the hook? If not, you could replace “recruits” with “men” in the next line.
“Things get no better when the squad finally sets sail. One of the recruits betrays them to the pirates and their ship is destroyed.” – Good.

“Janner must rely on the aid of an old shaman to infiltrate the pirate camp and free the boy.” – Is he alone here or still leading his band of recruits?

“However, when he learns the pirates are really a rival mercenary guild trying to start a war, Janner gambles the success of the rescue to unmask their plot.” – This doesn’t have the punch it could have. A way to grab someone’s interest is to end with a question (a strategy I use in my training materials all the time). Pose the end scenario in a question so the editor wants to find out what happens. Example: On the verge of rescuing the boy, Janner discovers the pirates are really a rival mercenary guild plotting to start a war. Will Janner honor his past love and save her son? Or is sacrificing the boy’s life to stop a war a regret he’s willing to accept?

I rambled a bit. I hope something here helps. I’ve been hearing about this story for years now and want to pick up a magazine to read it.

X is the main guy; he wants to do:
Y is the bad guy; he wants to do:
they meet at Z and all L breaks loose.
If they don’t resolve Q, then R starts and if they do it’s L squared.

Basically, it should be a happy medium between a synopsis and back cover copy. I’ve found I tend to lean toward the synopsis end of the continuum, so your observation does make sense.

With all the different concepts (love interest, rebellion/spy, master-mentor, unwitting allies, etc) and plot twists, I can see how an editor who may be looking for something a bit more straight forward could shy away from it.

You could do a very interesting short story just focusing on the old relationship and the challenges your protagonist faces going to save a son that maybe should have been his. It really gets muddled with the “And on top of that, THIS!” and “But wait, there’s even MORE!” The love interest part mentioned at the beginning is likely to be lost in the din of the rival guild plots that must be unmasked.

My opinion, anyway. You may have the talent to pull it off, but will an editor take that chance?