If kids are somewhere down the line/not in the immediate future, I'd take the Swiss option short term (1-3 years), save up, and then take it from there.
If your plans include enlarging the family ASAP, I'd probably take the German option now - money goes further, better/cheaper family-friendly options (parental leave, childcare, etc.) for dual-working parents.
I would say you live in the best city in Switzerland for a non-EU foreigner. Chur is boring, small minded and has little future, we have several young people from there working in our office in Zurich. They are very attached to Graubünden, but see it as hopeless for their personal future.
Manheim is ugly - lots of WWII damage, but is centrally located (excellent airport in Frankfurt, top notch train hub, Mainz, Darmstadt, nature (Weinstrasse and Odenwald) and excellent universities in the area. It's a very dynamic area, lots of foreigners. Much brighter future than Chur and much larger (300'000 inhabitants).
Pay is also better in Manheim for you, there you have the chance to buy a nice house and raising a family in Germany will be much easier. But again, both place are not Lausanne or Zurich in Switzerland or Munich, Berlin, Cologne, Münster, Freiburg, Hamburg or Dusseldorf in Germany when it comes to quality of life or openess to foreigners.
Germany 68k = approx. EUR3k/month net. Maybe more, depending on health insurance. I might have calculated this wrong, it sounds too low.
Switzerland 90k = approx. CHF5.5k/month net
With regard to living:
Chur is a very quiet place. It is picturesque, and has the honour of having HR Giger's ALien bar (he was born in Chur). However, that is not really enough to live there for a while. If you like a quiet life and want to spend a lot of time becoming an expert skier in the most (IMO) beautiful swiss region, easy access to Engadin, etc., it is great.
Mannheim: it is a bit brutal but is an actual city so will have a bit of life to it. If this was the choice, I would instead live in Heidelberg which is just lovely, only 10-15 mins train to Mannheim commute (even by bike on the river is only 20km or so) and enjoy an idyllic place...while going to Mannheim to have some life. You can get a nice apartment in old town Heidelberg for 1k a month, and have plenty of euros to have a great life.
http://www.brutto-netto-rechner.info
Plus:
https://www.comparis.ch/krankenkassen/default.aspx
In Germany, if you have a job, the whole family is covered by the mandatory health-insurance.
In Switzerland, your wife (and each kid) would have to get their own (kids get a discount, though).
If you're into skiing, mountain biking, hiking or just generally like to be outdoors, Chur is probably better than Mannheim - they only get slush at best ;-)
Therefore if it's just about money, Germany has the better offer. Cost of living will be about half as much in Germany vs Switzerland, obviously even if considering taxes. Taxes are not 40-50% in Germany, but closer to 30%. And as per usual, a German net salary is NOT the same as a Swiss net salary.
Walking away with 3000-3500€ net in Germany (after taxes, social contributions and health insurance) is worth A LOT more than walking away with 5000-5500CHF in (after the same deductions incl health insurance with low deductible) in Switzerland.
Neither Chur nor Mannheim are particularly interesting or exciting, so that can't be the deciding factor. If you are outdoorsy, Chur is likely a nice base as it's obviously right by all the mountains and lakes you could wish for, and it's still close enough to Zurich and other larger cities, so that would be an argument pro Switzerland.
If intending to have a family, with a working wife/mother, better to stay in Germany - longer maternity leave and considerably lower child care cost.
Up to you which of these factors are more important. Quality of life is based on much more than just salary. Well it should be anyway. Priorities are obviously personal though.
Tom
I visited Chur last year. The city is very nice but also very small. Boring. For Switzerland it is in the middle of nowhere. But than again Zurich is only an hour drive from Chur... Road to south to Ticino is simply spectacular...
CHF 100-150 per day are normal here. Definitely a cost to consider if, as said, children are planned and the mother intends to (continue) work(ing). Switzerland is not the place to go if the cost of and access to (semi-affordable) childcare is a serious factor.
I would also look into citizenship/passport situation in both countries for you and your family. Europe is a scary place currently (AfD, SVP, UKIP, Front National), it's important to have the protection a citizenship grants. You will have more practical advantages with a German/EU passport, but it can be that you get the Swiss passport quicker because you have studied here. But at least as important are children and your wife and how quickly they can get citizenship.
In Germany you can get also https://en.wikipedia.org/wiki/Blue_Card_(European_Union )
While no company can guarantee a work permit, the multinationals don't usually run into problems getting them.
(When early retired @ 60+. No wealth tax, no eigenmietwert, 2/3nd pillar taken as lump sum and taxed in CH before the move)
Also very nice houses available at 300K to 500 K.
And I do like the North Sea ..
Jos
But I do see your point as I have a place in Berlin.
In this situation DE is better than CH, unlike when you're still working.
Alas a similar move to NL would be economic suicide.
Legallly Krankenkasse would have to remain based in CH, so no savings there.
Jos