This is the definition of a Marty Stu (male version of a Mary Sue) from tvtropes.org:
"...he’s not a human so much as he is a Ken Doll, except instead of plastic, he’s molded from untempered wish fulfillment." Marty Stu, however, is usually restricted to being a creature of action since men who do not take an active role in dramatic events are unmanly and, by definition, not perfect (Non-Action Guy tends to be looked upon with disdain). So Marty Stu is the personification of action, action and more action. Or, if he is of an intellectual bent, he thinks his way through problems, inventing whole new branches of science and technology in the process.
While I would agree that Henry was generally, although not always, the go to guy for many things science on the show and also provided a sort of moral compass for it, he was hardly morally flawless or as "self sacrificing as Jesus." As early as the end of season 1, he was willing to risk collapsing the space time continuum just so that he could try to save Kim, his love interest at the time. He put the lives of everyone in the entire town at risk so that he could save his wife. That's hardly the behavior of a character who takes no active role in dramatic events. He also was not above holding massive grudges as he did at the end of the season 2 premiere episode when he erased Carter's memory of the previous timeline while refusing to erase those memories for himself purely out of anger and resentment that Jack had prevented him from saving Kim. This culminated in his season 2 partnership with Beverly Barlow, one of the primary villains of the show, in an attempt to find out what happened to Kim.
Even when Henry tried to consciously remain morally superior, he was shown out on the show to be sometimes overly idealistic as was the case on the episode in which they were all trapped inside Jack's house. Henry and Stark had a pretty decent heart to heart about how Henry was disappointed in Stark for losing his scientific purity, so to speak, while Stark shot back with the fact that he took the job at Global Dynamics so that Henry could keep his ideals intact. Henry's ideals had made him somewhat of a pariah in scientific circles. Stark admired Henry, saw him as a mentor and wanted him to be able to continue doing the things he loved to do, so he took the job of doing the dirty work at GD so that Henry would have a place to belong in the town. Henry may have been somewhat of an idealist, but it was clearly shown on the show that those ideals came at a price.
So, while Henry could be accused of being a jack of all trades and possibly even a moral elitist at times, he was hardly a Marty Stu. I actually think that the show was very good about avoiding the Mary Sue/Marty Stu trope given how many so-called geniuses inhabited their character roster. No one person on the show had all the answers, and everyone was allowed to be flawed in some way.
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