Q1) You can book online for round-trip service. Their payment is taken online at the time of booking. Sunshine Flyer says that they only accept reservations up to 4 days in advance, so I don't believe you can just walk up and book. Even if it is allowed, I highly doubt they'll take cash at the airport. I've taken both Mears and Sunshine Flyer and both seem to be relatively on time when headed back to the airport. Both also say that they pick up 4 hours prior to international flights. You'll receive an email the day before stating your pickup time.
Q2) Sunshine Flyer only serves the Disney owned resorts and Shades of Green. Mears does provide service to many of the off-site hotels in the Disney Springs and Bonnet Creek areas. Mears does technically serve Universal, but it's a different service so there should be no reason Universal and Disney get paired together on the same bus. In my experience, they tend to only mix resorts that are in the same general resort area. Regardless, the pickup time should be set to accommodate stops at other resorts and I haven't had an issue arriving to the airport on time.
Q3/Q4) The smaller shuttles really just depend on demand and driver availability. Ultimately you're paying for the same service, regardless of whether it's in a full sized bus or a large van. As long as you don't have a disability that requires a lift, your vehicle will simply be whatever they deem the best for that route at that given time of the day.
Q5) Like I said, I've taken both Sunshine Flyer and Mears and both have had their successes and hiccups since beginning operation earlier this year. I don't think that one is necessarily any more reliable than another one, the main difference really just comes down to what you're wanting. I do believe that Sunshine Flyer has a bit better customer service and theming (though I've found the theming to be rather inconsistent). The communication with Mears can be a little hit or miss at times, but the main benefit that offer is 24 hour buses, as Sunshine Flyer only operates from 4am-11pm daily.
Hopefully that helps answer your questions.