The Democratic and Republican parties did submit the required papers by the deadline, but with blanks where the nominee names would be, since neither had been officially nominated. As soon as the conventions were over, both parties submitted amendments to their filings to fill in the names.
According to at least one source I found, this kind of amendment is legal in Pennsylvania (where it happened before), but may not be in Texas.
What's clear is that both major parties did make a good faith effort to comply with the law, but with the dates of the conventions, they were not able to.
So, who's at fault? Texas, for having too early a filing deadline? The major parties, for having late conventions?
I would argue that to take them off the ballot would be the fairest option, in principle, but in practice, it will merely create a major headache for election officials who would then have to tally millions of write-in votes for Obama and McCain.
Prediction: If the court even hears the complaint, they dismiss it because of the implications for the actual election.