please point out to me where the Lotus Sutra isn't accepted as the final teaching of the Buddha (actually the last sutra is the Nirvana Sutra which is regarded as a colophon to the Lotus Sutra). This is accepted in Mahayana just like Maitreya is the Buddha of the future.
A simple answer would be, as you say, the Mahayana Parinirvana Sutra, or the various school's Mahaparinibbana Suttas in the Agamas, or the Sutra of the Buddha's Bequeathed Teaching (遺敎經) which are popularly known as the final instructions of the Buddha in the East Asian traditions.
Part of the Lotus Sutra's supremacy centers around classifications of the teachings such as the Five Periods of the Teachings (五時敎判). Other traditions, such as the Tibetan schools, tend to classify the teachings from the perspective of the Three Turnings of the Wheel. The first turning would be the teachings on the Four Noble Truths and suffering. The second turning is the teachings on shunyata, based on the Prajnaparamita Sutra. The third turning would be the teachings on Tathagatagarbha, based on sutras such as the Lankavatara and Samdhinirmocana. Other third turning sutras are the Shurangama, Srimaladevi Simhananda, Mahaparinirvana and the Lotus. Different Tibetan schools hold different turnings to be definitive. My school takes the second turning as definitive, the third turning being a provisional teaching for those who were afraid of the (incorrectly assumed) nihilism of the second turning. Others hold the second as definitive, while still others take both second and third as definitive.
The problem with all these classification systems is that they are historically inaccurate. The Pali canon teachings span the entire teaching career of the Buddha, up to his passing. So we have the rather strange situation of multiple Pali and Sanskrit Mahaparinirvana Sutras (I'd be interested in knowing the basis for calling the Mahaparinirvana Sutra a colophon of the Lotus Sutra, since the Contemplating Samantabhadra Sutra is often considered to be the concluding text of the Lotus Sutra). Also, there are those who state that the Avatamsaka Sutra was the complete and full expression of the Buddha's enlightened realisation, but since no one could understand his teachings at that time, he spent his teaching career preparing beings for such a teaching. So this question of the final sutra is not quite that simple.