Revised 1 week itinerary - Advice on feasibility

Hi I'm going on a 2 weeks trip to Switzerland & Germany in mid April, need some advice for my Switzerland leg, especially on the Lucerne & Lugano part, should I give up 1 of them?

I'll be using a 2 day flexi pass for this trip

Day 1: Fly into Geneva, train to Lauterbrunnen (use flexi pass). Stay in Lauterbrunnen
Day 2: Stay in Lauterbrunnen
Day 3: Stay in Lauterbrunnen
Day 4: Train to Lucerne. Stay in Lucerne
Day 5: Train to Lugano. Stay in Lugano
Day 6: Take Bernina Express to Chur then take train to Zurich (use flexi pass). Stay in Zurich.
Day 7: Bus from Zurich to Munich

With this itinerary I believe it gives the most value for my flexi pass as I get half price fare in between the 2 dates which I use them. My main question is that should I stay in Lucerne & Lugano for 1 night each or skip 1 of them and stay in the other for 2 nights? My other plan is:
Day 4: Train to Lucerne. Stay in Lucerne
Day 5: Stay in Lucerne.
Day 6: Taking the morning train to Lugano followed by Bernina Express to Chur and train to Zurich. Stay at Zurich.

Thank you! ^^

GVA - L'brunnen: the most scenic itinerary goes via Montreux - Gstaad - Zweisimmen.
Lugano is worth a full day. Leave Lucerne at 7.47 (direct train).
Day 6: it might be much more attractive to sleep in the St. moritz area than at Zurich.

Meckerdv are you referring to the golden pass line from Montreux to Lauterbrunnen? I was thinking of doing the Mount Rigi or Pilatus round trip in Lucerne hence I thought of staying there for 2 nights and taking the early morning train to Lugano before immediately catching the Bernina Express bus at 10 am. In that case I would be able to use my flexi pass for the Lucerne-> Lugano trip too.

What would you recommend to do at Lugano? And do you know if the bus in Lucerne runs early in the morning as I might need to take the bus to Lucerne's train station from my hostel to catch the 6am train to Lugano assuming I stay in Lucerne the night before.

I know nothing about a 2day flexipass. May be you have a look at the official Swiss Pass site:
http://www.myswitzerland.com/en-ch/transport-reisen/billette/swiss-flexi-pass-en.html
In order to catch the Lugano - Tirano bus, you have to leave Lucerne at 7.18 or 6.18.
Lucerne citybus timetable:
http://www.vbl.ch/fileadmin/customer/Fahrplaene/Liniennetz_und_Zonenplan_2014.pdf
http://www.vbl.ch/fahrplaene/online-fahrplan/
Once you know the name of your bus stop, ypou can enter it directly in http://fahrplan.sbb.ch/bin/query.exe/en by precceding it with the word Lucerne, for example
from Luzern, Matthof
to Tirano
via Lugano

It doesn't make any sense to sleep at Zurich, if you want to go to Munich after your Bernina-Albula-Express ride:
Tirano dp 14.33 - Chur 19.03/19.12 - St. Margrethen 20.12/20.55 - Lindau 21.27/22.09 - Munich ar 0.57
Fares for the St. Margrethen - Munich ticket start at 43 EUR.
If you want to take the bus, leave St. Margrethen at 20.20 and arrive at Konstanz at 21.33. Sleep there and board theMunich bound Fernbus the next morning. Fares start at 11 EUR
http://meinfernbus.de/booking/search?route=Konstanz-M%C3%BCnchen&from=90&depart=10.04.2014&to=94&adult=1&children=0&bikes=0