Using the spell to gain extra Natural AC seems like the most obvious use. Lizardfolk are Humanoid, with +5 Natural Armor, and Troglodyte has +6. Both good choices. You get to keep and use all your gear and gain lot's of AC bonus for the cost of a low level spell. Their natural AC even stacks with magic items that grant it, so it's a high quality bonus.
Having the ability to become amphibious (Aquatic Elves) isn't exactly game breaking. There are very few campaigns where it really comes into play. I don't see a problem with them, though others might.
The winged elves of Faerun were mentioned as a Humanoid that can fly. Some see this as a problem, since the Alter Self spell lasts longer than Fly, and is a level lower.
What are good ways to control this, organically? That is, how do we limit this within the game, rather than simply by DM fiat?
One way I've heard used is to ask, "Has your character ever heard of/seen such an Elf?". That, sadly, is solved with a Knowledge Nature check. The DC to know about a creature is based on their hit dice, so the Avariel aren't exactly hard to have heard of. Even applying a circumstance modifier for "Rare and reclusive" doesn't help all that much.
Another way is to simply say, "That's from another game world. we aren't using Faerun", though that borders on the hard "Because I said so" that I'd like to avoid.
The only Large Humanoid form I'm aware of in the MM series is one of the Naga, and I think that's an error.
Small Humanoids are easy to find (Halfling or Gnome), but I don't know of any other non-erroneous Large ones. Half-Ogre doesn't work, since the spell forbids changing to a templated creature.
Does anyone know of a Large Humanoid in the game?
Does anyone know of another winged/flying Humanoid in the game, other than the Avariel Elf?
Does anyone know of a Humanoid with useful racial Feats, such as Tracking?
What other useful forms are there?
What other troublesome forms (from the DM/game balance point of view) are there?
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