Wow, trip of a lifetime, eh? Congratulations. I wish you good shoes, resilient stomachs, stamina, and much patience and good humor.
With this much moving about, pack light. Pack, throw half of it out, pack again. Repeat. A cabin-legal carry-on plus a smallish daypack (bookpack, crushable slingpack, etc.) should be all for each of you, otherwise you'll get seriously ticked off after the first week of schlepping. They sell anything you need that you didn't bring, if you really need it…
The Spain portion could do with some changes. You're so close yet not going to the super targets of Cordoba (Mosque/Cathedral Mezquita) and Granada (Alhambra)? In many seasoned travelers' opinions these two rival or even outweigh Sevilla!
Day 20 Seville, on your schedule, isn't really a day at all, whether you get there by train or plane from Madrid.
I see that you're aiming at a bit of well-earned R+R on Ibiza, but a couple of those days should go towards the south of Spain. And you can bypass Valencia by flying to Ibiza.
Days 17-18-19-20 Madrid
Day 20 take a late train to Sevilla, like the 18:00 (arr. 20:30) or the 19:00 (arr. 21:30) - you get there and check in before dinner time (remember, dinner starts at 10PM in Spain).
Night of Day 20 and again of Day 21 sleep in Sevilla, to have a full day there
Day 22 pick up a car and drive to Cordoba (about an hour and a half), then after visiting the Mezquita drive on to Granada.
Day 23 visit the Alhambra (book way ahead, make it a morning appointment, you get assigned a specific narrow timeslot to enter the palace inside the grounds, but you can spend as much time in the grounds themselves as you wish as long as it's morning or afternoon as per your ticket).
Late on Day 23 fly to Ibiza with the 19:00 departure from Granada (arrives either 22:50 or 23:25 depending on which connection you book - see www.vueling.es). Or sleep in Granada and fly the next day - no need to make the much longer journey via Valencia if that's all you wanted to do in Valencia.
Then again, you could turn this around, by going from Madrid first to Granada, then driving via Cordoba to Sevilla, and from Sevilla you can fly to Ibiza. Three days a week you can take Ryanair (nonstop but with severe luggage restrictions), or you can make it a two-hopper with Vueling.
The fastest train from Sevilla to Valencia takes 3:30, the others take 4:33 or 4:45. The 17:22 arrives at 21:12.
From Granada you could take the night train to Valencia, saves a night in a hotel. It is called TRENHOTEL, train nr. 894 leaves Granada at 21:30 and arrives at 04:10 - you can sleep on the train. Then explore Valencia at the sun comes up, and by 12:30 you can be on the ferry to Ibiza.
More info on trains at www.seat61.com/Spain-trains.htm#.UYk8nb9YVWs - also guidance for booking online.
Instead of basing yourselves in Geneva (not too attractive a city), book a room near Montreux - up above in Glion or Caux, both with splendid views across the lake onto Mont Blanc even if it is foggy down below, or down by the lake, Montreux -Vevey or in between.
To access the Mont Blanc region you take the train from Montreux to Martigny and switch to the Mont Blanc Express (sometimes substituted by coaches for a stretch that may still be under reconstruction).
Check out http://members.virtualtourist.com/m/p/m/ea7ae/ and also http://tinyurl.com/bll8rmh
Above Montreux is the wildflower paradise of Les Rochers de Naye, there is a cute mountain goat of a train that goes up, see www.goldenpass.ch/?OrgID=7
Near Montreux is the famous Chillon castle (www.chillon.ch/en/index.cfm) - reached by trolley bus or by public boat - see boat schedules at www.cgn.ch.
Note that the lake Geneva is only called that in English, when you look up schedules or directions it helps to know that locally it is the Lac Léman - or, in German, Genfersee.
To get to Milano there is no point in doubling back to Geneva, you can fly from Zürich (the bigger airport anyway), or take the fast trains from Zürich through the alps (past Lucerne and through the Gotthard tunnel).
Your routing is not really efficient after that. I would go from Milano to Rome, via Pisa. There are a few trains, Intercity (slower than the Frecce which means arrows, the express trains), that require no change between Milan and Pisa, they take about an hour longer than those where you switch trains in Florence. Either way, you can be in Pisa long before lunch, leave your bags at the station, and walk to the leaning tower and cathedral and baptistry, best through the old town by crossing the Ponte di Mezzo.
Then take one of those trains that go from Pisa Centrale station to Rome not via Florence again, but down the coast, like the 13:52 that arrives in Roma Termini at 16:28, or the 15:10 (arr. 18:18).
Then after Rome I suggest at least two nights - one full day at the very least - in Florence, take these days away from Milano where you don't need as many days (unless you have specific daytrips planned?).
Then from Florence to Venice, then to Innsbruck (if you really wish…) and then to Munich, then to Salzburg and on to Vienna, then to Prag and Berlin, in that order.
Why Frankfurt? Unless it is to begin a leisurely trip down the Rhine valley to Cologne, but that's a different story and requires even more time. Skip Frankfurt, it is a rebuilt nondescript city full of office buildings and not really much more, not when compared to many other destinations for which you don't have time (not on this trip, anyway - you'll be back!!!).
Hope this helps.