As Arno says, you are dealing with personal preferences.
Zermatt and the Jungfrau region both offer high Alpine experiences. There is more available at lower altitudes near the Jungfrau, and a greater variety of mountains, views, and hikes than at Zermatt. However, Zermatt has some spectacular views and hikes.
The walk from Männlichen to Kleine Scheidegg ( in tha direction) is wonderful for all ages, and easy. It is possibly the best easy mountain walk in Switzerland....at least it is high on the list. It has the nickname "The Grannies' Trail" because it is easy...as long as you are used to the altitude and walk downhill toward Kleine Scheidegg.
There is a good chance that trail will be open, though there are no guarantees in October. The cableways operate regularly until October 23rd, so you should be able to get there.
(in this thread, Kim has obligingly listed the schedules for the cableways, etc.-
I attached a picture or two
Luzern is different. Not just because of the lake, and lake cruises ( which are on a reduced schedule in October) but because there are two different kinds of mountains nearby - the Rigi, and Pilatus. The town itself has memorable tourist sights and experiences.
So, based on my personal preferences, which do not focus primarily on the Alps,
I'd split my time between Luzern and the Jungfrau region, and skip Zermatt. Part of my logic is that you are trying to see a whole lot of things in a short time, and may not really get to experience them. To balance that, riding the trains is a pleasant part of the travel.
if you decide to change and go to the Jungfrau for clear weather on a day when you have scheduled another location, trains from Luzern to Kleine Scheidegg take thre hours and 15 minutes. Trains for Zermatt take about 3 hours 40 minutes.
So, it is really a matter of personal preferences, and no one route is "better" than another.
<<"Also how do we go to Zurich from Zermatt. whats the fastest and the most scenic route?">>
There is no such thing. ;-)
The time table automatically gives you the fastest route:
www.myswissalps.com/ti metable read the instructions; note that default mode is fastest.
The default route is 3 hrs 11 minutes via Bern Thun Spiez, the new "Lötschberg basis tunnel" to Visp and Visp to Zermatt.
It avoids the most scenic stretch along that routing, which s to use the old route over the Lötschberg via Kandersteg, and which adds about one hpour to the journey.
If you want the most scenic fairly direct route that can be reasonably accomplished, travel fromZürich to Luzern, take the Luzern Interlaken Express via Meirngen on the Golden Pass route to Interlaken Ost, then to Spiez, then pick up the "Lötsberger" train over the Lötschberg to Brig, then Visp, the n on to Zermatt.
I did not check it, but it probably adds another hour or two.