Both resorts are good, but riverside is in our opinion better of the two, hence why we have stayed so many times there.
The bus service between the resorts and the parks is pretty good, and problems often over-exaggerated. FQ, as has been mentioned already, has the advantage as you are first on going to the parks, and first off coming home.
Buses to MK as you have seen are separate - except at quieter times you may find its shared.
Buses from EPCOT at night can be separate depending on time of year / hotel capacity.
Remember, because the resorts are next to each other, if at the parks one bus is taking its time to come, then hop on a bus for the other resort and either walk or get the boat between them. I did that a couple of times last year out of MK - although in the end I didn't save myself a huge deal of time.
If there is a delay at the park, I just walk to the dispatcher and ask when we can next expect a bus, as sometimes the system seems to miss one out, and so they can allocate the next bus. At night, you may have a longer wait as you tend to find they'll wait for the low floor buses to serve RS and FQ as they have a larger capacity - that of course is dependant on people moving to the back and standing two abreast in the middle!
We stay in the first couple weeks of July, and only a couple times over teh two weeks during the day would we find a longer than 20 minute wait from the resort.
The other thing to consider is people have different tolerances when it comes to waiting and what they think is poor - such as sharing with a resort. The loop around Riverside doesn't take that long - 10-15mins tops - so long as no wheelchairs which add time. While some from FQ might moan at having to go round, its a godsend for those RS guests who are around the perimiter and saves them a long walk from the front entrance. Of course, it is worth remembering that the EPCOT resorts share buses to the parks, and that is a much bigger time going around the resorts that POR. The same can be said for the MK resorts to Downtown and some other parks like MGM. And those guests are paying much more than we are.