Final Itinerary Swiss Honeymoon Trip 2 October to 10 October

Keep your plan flexible enough to take weather into account. If the weather is nice, go to the Jungfraujoch first opportunity. To get there from Wengen, you will take a train to Kleine Scheidegg then change to the train to the Jungfraujoch. On the return, you will again stop at Kleine Scheidegg, so that would be an opportunity to hike to Maennlichen in the afternoon.
Use the Bern trip for a bad weather day. If you don't have any bad weather, skip it. Why pass up beautiful mountain day for a day in the city?
The Brienzer Rothorn is on the way between Wengen and Luzern, so if you have good weather, you can stop there for a few hours.
I'm thinking you might go to Villa Honegg first, then to Luzern. Zurich airport is only 1 hour from Luzern. Not sure how you get there from Villa Honegg.
An 8 day Swiss Pass would work for you. You actually have 9 total days. The last day from Luzern to Zurich airport is not too expensive to pay full price after the pass expires. Part of my reason for doing Villa Honegg earlier. The Half Fare Card is usually the best value, but you will need to buy a ticket before each journey. You will still need to buy tickets for the Jungfraujoch, and the Swiss Pass only gives you a 25% discount, where as the Half Fare card gives a full 50% discount. But there is something to be said for the hop-on hop-off convenience of the Swiss Pass for most other trips.
In expensive places to eat? In Switzerland there aren't any. But most of your hotels should have a free breakfast buffet included in the price. You can buy picnic food at the grocery stores for hiking lunches. There is a Coop in Wengen. In-room dinner picnics don't sound very romantic on a honeymoon.

Wow thanks for the excellent replies. If I'm able to combine Jungfraujoch with Männlichen hike, I can use my day 4 for another hike.

Where could this be ? I have heard that First to Baschee is one of the most pretty ones. Can I go there from Wengen?

In my itinerary I have skipped Schilthorn but instead have Rigi, Titlis and Jungfraujoch. Am I missing something too much ?

Can I combine a hike on a day trip to Titlis??

What are the options for a rainy day in lucerne like you suggested Bern for Oberland ? Visiting Thun ??

If you're going to the Jungfrau in the morning, - take the train via Wengen to Kl Schiedegg and on to Jungfrau. Then on return, stop at Kl Schiedegg and do the Ridge Walk to Mannlichen. There's a gondola down to Wengen, which you can see near the downtown area of Wengen. Otherwise, take the gondola up to Mannlichen, do the Ridge Walk to Kl Schiedegg, and then head up to Jungfrau.

Other hikes - take the train down to Lauterbrunnen, and the gondola up the other side to hike in the beautiful Murren area. (Some say that side is even more beautiful.) Or, for something cheaper on your second day, we went for a hike outside Wengen. We stayed at Hotel Alpenruhe (nice hotel & location) and walked out Gallewedli Road and up behind Wengen for some nice views. On the way back down we found a drawing by Mendelssohn on the trail at a viewpoint: I studied classical music, so finding that the German-born classical composer Felix Mendelssohn was inspired by the alpine landscape and drew this depiction of Wengen in 1842 was special to me.

I second the suggestion of grabbing picnic lunch items at the Wengen Co-op. We actually spent less money in Switzerland than the Italy portion of our trip because we ate breakfast at our hotel, stopped at the grocery for items to eat on our hike. After a hike, we would relax with a glass of wine in our hotel room on our balcony overlooking the gorgeous valley & mountains, and then go out for a a normal dinner or split a pizza.

Is Gondola from Wengen to Murren covered by the Swiss Pass?

I would like to experience a good hike from Murren as well. How is the Murren to Gimmelwald hike as Steves recommends?