I don't think this is intentional. I think they actually do an amazing job with transportation at WDW.
You are right about taking a lot of time going back and forth though. We plan our days to go at park opening each day (the best time for rides) and taking a break midday anyway (while the parks are overflowing.) Then we return in the evenings for entertainment.
If you want to stay straight through, why not pack a lunch to take with you?