We have been fortunate to have found so many knowledgeable people on this forum. That said, I hope there may be one or two who would take the time to consider this: From your experiences, would you drive, fly, take the trains, or bus.... or combinations of these? We have our own car over here, but at our ages it becomes daunting: have the convenience of being able to stop for short side trips, vs the rather long drive. We have no tight time line. TIA Mike & Mary.
I would take the train to Paris and change there for the overnight train to Berlin. But there are other options available as well.
When considering the night train, think about the accommodation.
You don't say how old you are, but wording suggests that, like us, you may be getting on a bit!
We have been investigating sleepers, and think that reaching the upper bunk may be beyond us.
Driving would be about 15 hours - if we were doing that we would break it into four days with interesting stops.
By train, we'd do it in two day stages with an overnight (or two) somewhere interesting.
Or fly, with one change - c. 5 hours.
There is a flight on Lufthansa from Rennes to Frankfurt, then the ICE train to Berlin.
Or my own choice on the correct days of the week would be Rennes to Paris, the new Classic (as opposed to the Eurostar) train to Brussels, then the Prague bound European sleeper as far as Berlin.
You could may be do a side trip to Bruges (or elsewhere in Belgium) before continuing next day.
If you do Flixbus, apart from being a 19 to 25 hour journey you have to change at Paris (Bercy) which is one of the distinctly less glamorous features of Paris.
There is also a 0648 train from Rennes which connects with the day train from Paris to Berlin, or a 1600 Rennes to Strasbourg connecting with the Night Jet to Berlin.