Also having this problem! I ensured that Album and Album Artist were always the same, as well as giving all episodes in a single season the same Album designation, i.e. "The West Wing (season 1)". Under the video tab I filled in all the fields, using the actual title in the Episode ID field. Despite filling in both the Episode Number field as well as the Track Numbers for every episode correcly, on the iPad using Home Sharing the episodes came back in alphabetical order based on the information in the Episode ID field under the Video tab. Ridiculous.
But by placing the episode number (01, 02, 03 etc.) in front of the episode title in the Episode ID field under Video (while preserving the title in the Name field under the Info tab, as that is the information used to actually give a name to the episode on the iPad), the order of the episodes finally matched the chronological order (episode sequence). So now they are all in order now, with correct episode names (without the number in front of the names) in the correct season and so forth. Worked, but was quite time consuming.
Does anybody else get tired by all this? The Photo App has similar problems: everything out of order with no way whatsoever to put my own files and pictures in the order I want. It is quite infuriating. Where is the vaunted seamlessness, ease of use, intuitiveness and beauty the media and fan boys salivate over constantly? I'm sorry... but what is beautiful or intuitive about arranging episodes of media I purchased legally not in chronological order and in an order that does not even correspond with the data in iTunes, with no way whatsoever to correct the problem except via tedious and time-consuming run arounds??????? Perhaps a focus group or two would not kill Apple. All these little problems are really irritating: death by a thousand paper cuts. Samsung products start to look attractive, I couldn't care less about their legal squabbles.
But all in all... rich world problems.