The development of enlarge person in brief
The 3.5 revision saw the Player's Handbook (2003) publication of the 1st-level Sor/Wiz spell enlarge person [trans] (Player's Handbook 226–7). Prior to the 3.5 revision, the spell was probably the removed and vastly different spell enlarge that, as it had in previous editions, offered only a graduated increase to any creature or object's size based on its caster's caster level. For example, the Player's Handbook (2000) version of the 1st-level Sor/Wiz spell enlarge [trans] (PH 200) never actually says that the spell enlarge increases a creature's size category, and, instead, it provides a size bonus to a subject creature's Strength score. (You can hunt down that version on this site.) (This graduated effect, by the way, is mirrored in the now-obsolete Psionics Handbook (2001) by the effects of the 2nd-level psion and psychic warrior power expansion [psychometabolism] (73).)
Unlike Dungeons & Dragons, Third Edition proper, my understanding is that the 3.5 revision wasn't the product of even the largely low-level and largely non-destructive playtesting that accompanied Dungeons & Dragons, Third Edition proper. (Readers can learn more about Third Edition's development in, for example, these columns.) Instead, the 3.5 revision was the result of the experience and knowledge of its developers—particularly its architect Andy Collins—and feedback from fans, likely including some from the game's vocal fans on the now-defunct Wizards of the Coast message boards but almost certainly including some from players who participated in organized play experiences.
However, neither the spell enlarge nor the spell enlarge person is mentioned in, for example, the Revision Spotlight Web column or in the Revision Spotlight columns that ran in Dragon magazine from issue #304 through #309. (Even #307's column covering spells is silent on the enlarge to enlarge person revision.)
In other words, there's no way to know why the spell enlarge—that had endured virtually unchanged for over 25 years—was changed to the spell enlarge person, much less to know why the new spell only targets humanoids.
Now, steel yourself for pure and rampant speculation!
In a core rules-only campaign at low levels, a hypothetical enlarge creature spell could seem unbalanced
Many campaigns never see high-level play, so confirming that low-level options (like low-level spells) are balanced often becomes—intended or not—a design priority, and there's the possibility that at some tables a hypothetical enlarge creature spell could seem unbalanced.
For example, a level 1 druid doesn't typically have access to the spell enlarge person so that druid would likely also not have access to the hypothetical spell enlarge creature… but his wizard companion may. That level 1 wizard probably can cast only between 2 and 4 1st-level spells per day, but it can be valuable—and perceived as unbalanced—to use one of those spells to make bigger the druid's animal companion. That animal companion that could be, for example, a riding dog that the DM has ruled is trained for war; a heavy horse that is already Large; a Medium viper that has a poison bite that can deal Constitution ability damage; or a wolf that doesn't need to be trained for war to make trip attacks with its bite. When such a creature is the subject of that hypothetical enlarge creature spell, that creature's ability to down foes—or even just occupy space on the battlefield—is probably unmatched by most low-level and core-rules-only PCs.
With its duration of 1 min. per level but prohibitive casting time, it'd behoove the wizard to cast the enlarge creature spell on the animal companion when a combat encounter is suspected rather than actually during one. Further, because the animal companion is easily replaced (if not emotionally then at least physically), were it to die after being sent to take out the opposition, the PCs could knock off for the day and let the druid pray for a new one and repeat this process… possibly for much of the adventure. The PCs could end up putting themselves at little risk.
Some players would just call this smart play—like sending ahead a celestial monkey to scout for traps—, but some DMs would see this as an exploit. I can imagine to some DMs in the latter camp that the path of least resistance to rectifying this issue would be to adjust the hypothetical spell enlarge creature to what we know now as enlarge person. It's just a lot easier to convince a loyal dog (or horse or snake or wolf) to take on a group of orcs than it is to convince a human commoner 1 hireling to do the same, even if that hireling is the subject of an enlarge person spell!
Further, when evaluating a spell, a developer should also imagine it being cast by the opposition.
At CR 1, a kobold sorcerer 1 isn't typically much of a threat, but a CR 3 ogre can be terrifying to a party of level 1 PCs who will likely see one of their number die each turn they engage the ogre in melee. However, as a pair, the two creatures are an Encounter Level 4 encounter that the Dungeon Master's Guide on Table 3–2: Encounter Difficulty calls for a group of four level 1 PCs merely challenging (49). (Further, the DMG suggests that 3 in 20 of encounters be in that EL range!)
Hearing the party coming (the feat Alertness is default for a kobold), the kobold sorcerer can cast the enlarge creature spell on his ogre buddy before the party arrives. The PCs then must face a Huge ogre with a 20-ft. reach. In the confines of the typical dungeon, the typical low-level and core-rules-only PCs likely won't stand a chance. The same problem recurs with the ogre alone if it's equipped with a potion of enlarge creature, that potion having a price of just 50 gp.
Of course, these are both situational examples, and I'm certain readers can develop a host of answers, solutions, workarounds for each of them. The goal, though, is to show that it's possible—in a core-rules-only campaign at low levels—to view a hypothetical enlarge creature spell as a potential problem.
Seriously, though, in your campaign—that probably isn't just the core rules alone and that may not be low-level—, there's no way this writer can know if a hypothetical enlarge creature spell will actually be a problem.
However, for comparison, I'm pretty sure in many campaigns the enlarge person spell is not a problem.
The power expansion renders some of this speculation moot
The Expanded Psionics Handbook (2004) offers a way for any creature to embiggen itself: The 1st-level psion/wilder and psychic warrior power expansion [pyschometabolism] (XPH 105–6) both lacks the enlarge person spell's prohibitive casting time (the power's manifesting time is 1 standard action instead of a 1-round action) and lacks its restrictive targeting except that a creature that possesses the power can only use the power on itself. The tremendous downside, though, is the expansion power's duration of just 1 round per manifester level.
Still, while the expansion power's Range: Personal entry makes it impossible—even with generous psionics–magic transparency—to create a potion of expansion ("Spells with a range of personal cannot be made into potions" (DMG 286)), psionic tattoos—psionic potions in all but name—can specifically be used to manifest on the bearer powers (like the power expansion) that possess a range of personal: "Powers with a range of personal can be made into psionic tattoos, but they cost double the price of standard psionic tattoos" (182). Thus by paying 100 gp per round it desires to be affected can any creature—by taking a standard action, touching the tattoo, and willing it to manifest the power—change size once.
