Personally, I suspect the real reason Henge isn't used more often is because Kishimoto can't world build, with a patch in the form of making it so that holding a henge disrupts ones chakra enough to make other things difficult, and by the time they have reserves able to hold it for any meaningful amount of time they have better options.
I always figured Henge had the same problem a Fairy glamour has: Sure, it'll let you do just about anything, but it's really fragile. Come into contact with the wrong material or the wrong chacra or simply put to much stress on it and the whole thing breaks. Other techniques might not be as flexible, but they also won't break before you do.
I figure some variant of both of these possibly, plus definitely a matter of "it's not as easy as it looks." Mostly in terms of using it for a form that you haven't practiced with it before a lot. Sure, you can transform into the guy next to you when you have him right there to use as a visual reference. Making up a new look from your imagination though, or trying to get someone right by memory? That's hard. That's hella' hard. On top of that, it might be harder to keep it going when you're moving around a lot, as opposed to transforming and mostly just standing there. Or transforming and letting someone else do the moving for you, as in the case where Naruto henged into a shuriken for Sasuke to throw. Or in the case of when Naruto transformed his toad summon, if the someone else is staying in contact with you for the duration they might be able to hold you in a transformation while
you do the moving, but that would be highly situational.
Most shinobi might practice one or two alternate forms that they can use as disguises, and they might or might not know their teammates well enough that they can transform into each other as a tactic to confuse enemies. Going beyond that though, most people could only really hold a henge of some rando if they were like, a guard standing in one spot who they killed and replaced, or an inanimate object that they had one of already and they wanted to make it look like there were two instead of one and a person.
The idea that it takes effort to
maintain a transformation is also supported by the Third Hokage's battle with Orochimaru: Hiruzen's summon, Enma the monkey king used henge (in the manga it's specifically labelled as being henge) to transform into a variably-sized adamantine staff, something that given mythological references, Enma was probably quite familiar with, which Hiruzen then used as a weapon. When Orochimaru blocked it at one point with the edge of the Kusanagi no Tsurugi, a blade that could damage such a staff, Enma had difficulty holding the transformation due to pain, and partially untransformed for a moment.
If it really is a physical transformation, then there is a lot of substance a ninja can transform into to escape various danger.
Enemy tied you up in ropes and chain? transform into liquid or gas and escape.
Enemy blast you with million volts of electricity? transform into a gas or block of rubber
Enemy blasting you with fire? transform into water/rock.
Enemy release poison gas into a room you are in? transform into a chair and wait out until the gas dissipates.
Enemy throws those ninja star or knives at you and you have only seconds? transform into block of stone
So, If it is an academy jutsu, I would wonder it is because of its versatile application and not due to being an easy starter jutsu for a child to learn.
All but one of those are better served by using the Substitution, a different one of the Academy Three that is specifically designed for such things. The last one, with the poison gas, you probably could use it to reduce the amount you breathe if you notice quick enough before you breathe in too much of the gas, but such an occasion never came up in canon. Presumably, if it had, Kishimoto may have had someone use henge in that way.
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