Is Berlin and Munich doable in a single weekend?

I am German, and I have lived in Munich for a while. Let me say that you can't see much in two days. Instead of trying to do two cities, why not do just do one well? Munich is richer, more conservative, with lots of culture, a beautiful town full of beautiful places in the setting of the nearby Alps. Berlin is a young, international city with a diverse mix of innovation, creativity and historical places (and a bit less expensive).

It depends on what you mean by "doable".

Berlin really needs several days IMO. You need to go to the Berlin Wall history museum, the East Side Gallery, the Memorial to the Murdered Jews of the Holocaust, The Topography of Terror. I'd add in the Reichstag building, Brandenburg Gate, and of course personal favorites, if you're a geek, like the Game Science Center and the Computer Game History Museum. Ideally you'd check out Mauerpark Flea Market on a Sunday. And that's the short list. There are other museums, areas of the city to stroll around, etc that I personally found worth seeing.

Even without the geek stuff though if you crazy rushed you could do the first things in 1 day. I personally couldn't do it.

I haven't been to Munich.

I live in Berlin and come from an area down south close to Frankfurt.

In addition to Alexander and Willeke´s great answers I would add the following:

1) It is doable seeing only main attractions, I think but it will be really hard as everyone mentioned but definitely doable. I do sightseeing with some of my visitors in Berlin by foot or bike in around 6 hours and we have covered the majority of main attractions.

2) I would suggest FRA->BER->MUC-FRA Besides the Flix bus option I would also consider BlaBlaCar. Which can save a lot of time as it is car sharing and therefore way faster in most of the cases. Which will give you then more time in the cities. Also I would stay longer in Berlin then because of the prices for Oktoberfest in Munich on that day.

3) These passes only exist for slow trains and not the ICE. So you would have way longer travel periods and less time in one place.

Hope that BlaBlaCar will help you and save you some time traveling so you can make the most of it.

If you can really sleep in buses and there are tickets for the buses you plan to take, you can do it.
But most people will be broken after a night in a bus, sleep only little or lightly and will not do well to do it more than one night running. Trains might be a little better but not by enough and they are more expensive.
There is no direct overnight train from Berlin to Munich I can see, (although there might be one on other days) and your easiest option is leaving Berlin after an early dinner to arrive in Munich about 7AM, or leave a bit later and 'change' with a stop over of a few hours in the middle of the night.

You will have a few hours, likely more depending on the time the buses arrive and leave, to see the main sights of the cities.

The easy option is to do a tour, although you will see more buses than you should on this trip.
The other option is to walk, either a tour or by yourself, but you need to do your homework to see what there is to see in the cities.

I do feel that you will not get much out of this trip besides bragging rights.
If you really want to do it, book all bus and/or train tickets in one action, so you are not ending up with two out of three tickets, making those useless. Do your homework, get an (online) guide for each of the cities and read it. Or just search online for tourist information.
As you are in Munich during the festival, consider booking into one of the beer garden tents as just walking in seems unlikely, specially as you have such limited time.

If you had a day more I would suggest flying from Berlin to Munich, but as flights eat much more time than the actual travel time, I fear you will not win anything but lose a couple of day time hours for getting to and from the airport, and will not be able to sleep much or at all even for an early morning flight. A late night flight will solve that but has the potential to leave you with only expensive transport from the airport.
Besides, with the short period left before your intended travel, it is very unlikely that you will find cheap flights anymore.

I have been in Berlin for four weeks(!) in school summer holiday 2004 (age 18). It wasn't boring at all during that time, although I must admit that I spent some days in museums and at Wannsee Tegeler See, as well as at the "open doors" weekend of the federal government.

But still, Berlin has enough attractions to entirely fill your weekend - museums, fountains and churches not included. Checkpoint Charlie, The Berlin Wall, TV tower, Reichstag dome, to name a few. Not to forget that you will be in a bus during Saturday night, when every sane Berliner is enjoying themselves. Cheap hostel bunkbeds in nightlife locations, on the other hand, start around 15€ per night.

Munich also has enough attractions for a week-end, if not longer; but if price is important, I wouldn't go there during Oktoberfest, with regular hostels starting around 100€ for a single night.

You should really consider doing a single city now, and keep the other city for your next visit to Germany.