I would definitely recommend the factory service center. We've taken both our motorhomes there whenever they required service I was unwilling to do. They have the best trained and most courteous technicians in the business. They also have the best parts inventory since the motorhomes are manufactured about 100 yards from the service facility.
They will do whatever type of service and repairs you want. They will give you an estimate as to cost and the amount of time required to complete your requests.
Over the years we've been there probably half a dozen times and have never been disappointed.
In 16 years of owning Winnebago products we've only been a dealer one time for anything other than buying a motorhome. That one other time was to replace a defective propane tank. The dealer did excellent work, but had to wait several days to get the new tank shipped from Forest City. Since it's almost the same distance from our home to either the dealer or Forest City we now only go to Forest City. There's never been a wait for parts, or the need to get an OK from a district rep to proceed with a job.