If I'm not mistaken the reason is to signify "her" independence as foot binding was a common practice in China. It denotes a depiction that is anti-Confucist and pro-Buddhist. In addition, the portrayal of deities having large feet is fairly common to other imagery as well. Having large feet means you can trample things underneath them... like other gods, or worlds, or realms, etc.
In his book "Hinduism and Buddhism" Sir Charles Eliot states that the creation of female Guanyin was probably "facilitated by the worship of Tara and Hariti, the fatter is frequently represented as caressing a child." In his view the Chinese religious sentiment required a Madonna and it is not unnatural if the god of mercy who is reputed to assume many shapes and to give sons to the childless came to be thought of chiefly in a feminine form.
An aspect that needs to be examined is the Chinese history during the Sui times. Yang Jian the founder of the Sui Dynasty, and who ruled as Emperor Wen was born in 541 in a Buddhist temple. Until the age of 12 he was brought up by a Buddhist nun whom he fondly called as the preceptor (A-che-Ii, Acharya in Sanskrit). Emperor Wen's queen Wen Xian came from a devout Buddhist family and was herself an ardent Buddhist who used to arrange Sutra reading in the palace in the evenings. Emperor Wen and his queen earned the name of ersheng --Twin-Sages. In the year 602 the empress died. The empress had been a strong influence on the emperor. On her death the court historian promptly declared her a Bodhisattva. In view of the strong influence of the empress on the administration and the spread of Buddhist ideology it is possible that the Bodhisattvaization of the empress could have marked the beginning of feminization of Bodhisattva.
Another remarkable example of feminine eminence a hundred years later was Empress Wu Zetian. Although according to the Confucian beliefs having a woman rule would be as unnatural as having a "hen crow like a rooster at daybreak", during the most glorious years of the Tang dynasty a woman did rule and ruled successfully. Women of this period enjoyed more freedom. They did not bind their feet nor lead submissive lives. Being born into a rich and noble family Wu was taught to play music, write and read the Chinese classics. When she was only thirteen she was recruited to the court of Emperor Taizong. When she was just an obscure imperial lady, she was loved by the young prince who later became Emperor.
To the south of Bodhgaya is situated the great cemetery bSil ba'i tshal. At this supreme place, one can hear the mighty voices of the gsbin rje. the magically powerful howling of the ma mo, the splashing of the sea of blood, the sputtering of the lamps fed with human fat, there is visible the coiling smoke rising from the evil burnt offering, there sounds the thudding of the male WW who are dancing a drum dance, the blaring of the thigh bone trumpets, the roar of wild animals; there is visible the quick flaring zip of the great scorching lightnings, is audible the fierce rolling of thunder and the crashing of great yellow meteors, the horrible laughter of the multitude of bdud and yaksas causes the earth-foun- dations to quake. At such a supreme place resides he, who has one face and two hands and possesses a terrifying body. His mouth is open and he clicks his tongue. His three eyes blaze like the fire at the end of a kalpa. He is of a vio- lently desirous nature, his body radiates and his limbs are strong. He roars like a dragon the horrible syllable hum. The colour of his body is a brilliant sky-blue, like the hue of the world-mountain Sumeru. In his right hand he holds the chop- per with which he cuts out the hearts of enemies — and he drinks blood from a skull-cup, which he holds with his left hand. The trampling of his feet causes the three realms to quake and in the countless worlds he reduces all kinds of evil powers to dust.
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A terrifying deity awkwardly dances on a lotus against a sea of flames. His scowling face is made more menacing by his third eye and flying hair. Clad in a tiger skin and sparsely ornamented, he is plump and heavyset and has disproportionately large feet. With his right hand he brandishes a chopper and with his left he holds a noose. He is one of a host of such terrifying deities populating the Tibetan pantheon; it is not possible to be certain of his identification.
http://archive.org/stream/spurgeonsgold000spur/spurgeonsgold000spur_djvu.txt
In very ancient times Ganesh was a god of harvest, mainly for the sugar-planters of the Dekkan and South India. The strongest ennemies of the farmers are the rodents and, in that time, people could not use pesticides; the elephant only seemed to be able to destroy rats by the bulk, thanks to his large feet stamping them. The elephant worship by farmers can be symbolized in these images where a huge Ganesh is sitting, in an unseemly manner, on a tiny mouse. The striking contrast is obviously wilful. There a superhuman creature, a god, shows His power on the noxious animal, like Shiva is dancing the Tandava on a vanquished demon. Nevertheless, the Ganesh rat is mainly found in western and south India (and Nepal) where Ganesh was a god of harvest. According to specialists, He is rarely seen in Kashmir and western Himalaya.
A final reason may be to compare her to an elephant, which is an animal that carries special signifiance:
In buddhist iconography we find the elephant-faced deity Gangpati or Ganesh as an emanation of the bodhisattva Avalokitesvara. Also in another aspect, representing the worldly aspect of the same evergy he is trampled upon by same other deities such as Mahakala, Vajra Bhairava and others.