Short 4 days trip in Switzerland - car or train

Hi and welcome to the forum.

Is one more scenic than the others?

Yes, definitely. The second one includes a part of the famous Golden Pass Line.

If you only compare costs and if the car turns out cheaper, rent that car. Roads are fine, but sometimes winding, cars are stick, automatic only if you pre-order. A somewhat similar route by car would be this one. Don't feel tempted to click the public transport button, it's foolishing you. Move the A sign to Biel/Bienne in case you start from there.

Considering the environmental aspect would however make you some friends in Switzerland, in this case, take the train. I for myself wouldn't do anything else, I even highly recommend the train if you want to make best out of your too short stay in Switzerland.

The best watch museum is at La Chaux de Fonds:
http://www.neuchateltourisme.ch/en/decouvertes/museums/clock-making-m-lanbspchaux-de-fonds.1500.html#tab2
http://www.mih.ch/mih/renseignements/default.htm
Scenic route from Geneva to la Chaux de Fonds
either along Lake Neuchatel
http://www.sainte-croix-les-rasses-tourisme.ch/en/page.cfm/Ete
http://www.neuchateltourisme.ch/en/decouvertes/town-heritage/treasure-chase-neuchatel.3542.html
or through the Jura hills along the French border: via Lac de Joux - L'Auberson (mechanical music instruments museum http://www.museebaud.ch/galerie-photos.php?langue=en
- La Brevine
http://www.neuchateltourisme.ch/en/decouvertes/watch-valley.html
The best Alpine area for hiking in May is the Swiss canton of Valais, that means the Valley between Lake Geneva and Aletsch Glacier (longest Glacier of Europe).

With the Family Card (can be got free of charge) Children up to 16 years travel free in Swiss trains, boats and buses.

There is no road along the most scenic leg of the Golden Pass railway line (Montreux - Montbovon). By car, you can either do:
Geneva - Montreux - Aigle - Col des Mosses or Col du Pillon - Gstaad - Interlaken (as suggested by a_p)
or
Geneva - Evian (southern shore of Lake Geneva) - Le Bouveret (Aquapark) - Aigle - Col des Mosses or Col du Pillon - Gstaad - Interlaken
or
Geneva - Vevey - Bulle - Gruyeres (medieval town, castle, cheese diary and chocolate factory at nearby Broc) - Montbovon - Gstaad - Interlaken.

Thanks for the recommendations!

I have booked a car. Will consider one of the suggested routes.

Once again,thanks for the recommendations. It was a great trip. We spent more money than expected due to rental of some extra stuffs, but we have much more freedom and it was relatively an easy drive. It was also much cheaper compared to the train.