I wouldn't call the Mears busses uncomfortable; they're motorcoaches with padded, high-backed seats. They do ride like a bus, if that's a concern. I would say that the Disney transport buses within the World are more likely to be uncomfortable. They have unpadded (or barely padded) hard plastic seats with low backs. There's also always a chance that there might not be any seats available on the WDW buses (not an issue on Mears).
To me, the Mears vs. Towncar issue boils down to three key points:
1) Cost: Mears charges per person, towncars charge per vehicle. With two people, Mears is a better deal. With three people it gets close to break even and at four a towncar almost always is a better deal.
2) Convenience: With a towncar, your driver is waiting for you at baggage claim and you leave the airport as soon as you're ready to go. On the way back, the towncar picks you up when you want. With Mears, you wait for a bus, then you wait for the bus to fill up, then you may have to stop at other hotels on the way to your resort. On the way back, they frequently want to pick you up four hours in advance of your flight.
3) Overall experience: The towncar is a much more civilized means of transportation.