I don't know what Littlefoot's mother's name is, but I might be able to narrow down a list of criteria for naming these characters...
1. Characters are often named after the species that they are: Sue is a Supersaurus, Pat is an Apatosaurus, and Bron is named after the Brontosaurus, which has since been proven not to exist.
There are exceptions to this, though; "Shorty" is a bit odd, as he is a Braciosaurus, which means "arm lizard." Ali is used here as a female name, such as ALIce or ALIson, not the middle-eastern male name Ali, which may stress the last I...
2. We know that "Littlefoot" is a bit of an odd derivation from "Sauropod" which literally means "lizard foot." Since that would be too odd of a name for the character, it was changed to Littlefoot. We know from the canon of the series that "Littlefoot" was a name that Bron was called when he was young, but it is unclear whether or not that was his real name and it was changed, or if it was simply a nickname in his youth. What is probable, however, is that Bron told this to his mate, and when the egg hatched, she named her son after what his father HAD been named.
3. Littlefoot and his family are Apatosauruses, which literally means "deceptive lizard" because the fossils found were similar to those of a Mosasaurus. It is sort of hard to directly name someone "deceptive", so a similar adjective with fewer negative connotations might be used, or the original Greek stem would be kept and not translated into English; Pterano comes from the Greek root "πτερ" ("Pter") meaning "wing".
4. To clarify the matter a bit, one has to consider that there were various species of Apatosaurus; the name "Apatosaurus" signifies a genus, not a species (from wikipedia.) The four species of Apatosaurus are "A. Ajax" , "A. excelsus" , "A. louisae", "A. Parvus"; which approximately translate respecitvely as "mourner", "to excel (or be good at)", "of Louis (from Ludwig, meaning "famous warrior"), and "small, little, cheap"; in the sense of being not important, not as in physical size.
The first possibility is probably inadequate; Ajax was a male name from the Homeric epic poems (Iliad and Odyssey) and the meaning of that name in no way suites Littlefoot's mother. Excelsus is a bit odd, and doesn't exactly describe her so well. Louisae is totally off... That leaves us with "Parvus"... which I believe to be the best choice for basing her name off of. It makes sense that a mother with a name meaning "small" and a father who WAS named "Littlefoot" (or was at least called that) should have a child with a similar name. Although the meaning of the phrase "small" is shifted in this case (from the meaning "insignificant" to the meaning "small in size"), it still fits the naming conventions well enough.
5. So, assuming that Littlefoot's mother follows that naming convention of most of the characters (named after their species, with modifications here and there), her name might be something like "Parva"; with is "Parvus" being given a feminine "a" at the end. I know that it sounds a bit like "larva", but it might just work...
It might be worth noting that "Parva" does not come up on any online etymology sites...
So, if I HAD to guess at the name of Littlefoot's mother, Parva would be my guess...
Alternatively, a name like "Lightfoot" might be used, in keeping with the theme of "little" (which light is similar to in the sense that something is light if it is not heavy, and little and light usually go together, although this is not always the case.)
"Parva" is probably no weirder than names like "Tria", "Tops" and "Pterano", all of which are names of characters in the series...
