First, I'm curious how you get from Ireland to Geneva? Which airline flies this route?
I see no reason to spend 3 days in Glasgow. Take off 2 days and add another one and tour the highlands in those 3 days. Going to Scotland and not spending any time in the beatiful country is a sin to the travel gods...
The same goes for Ireland. Take off a day from Dublin or Galway and go to Connemara or the Cliffs of Moher, or Arran Islands, and if you can take off time elsewhere you better do all 3.
And the same principle, but even stronger, goes for Switzerland. Are you not going to the Alps??? The travel gods will definitely kill you for a sin like that!
If you allocated 4 days for Switzerland, 3 of them should be in the mountains. With that time frame I would avoid Zurich alltogether and go to Luzern instead, and spend at least 2 days in the mountains of the Berner Oberland near Interlaken. Geneva is nice, but I would happily trade it for another day in the mountains.
That is... unless you're lucky enough to live near the Rocky mountains or the like and you have Alpine landscape in your back yard...
You could trade the Swiss Alps for their neighbors across the border in Austria, Italy or France, but I don't see those places on your schedule as well.
I agree with Kim about Manchester and Brugges.
If you look for a place to stop between London and Scotland, I would suggest York.
No need to stop at Holyhead. No need to go to Ireland by ferry at all, you better fly from London or Scotland or a dozen other places in UK. Buy tickets on line from
www.ryanair.com,
www.easyjet.com or other cheap airlines. You could fly for less than 20 Pounds between UK and Ireland, and between those and many destinations in the continent.
In Germany, I think you can do Munchen in just 2 days, and if you ask me, I would trade Frankfurt for Rothenburg, Heidelberg, Koln, or a day on the Rhine by boat.
Also, Brussels can be done in a day.
In Italy, if you take off a day from Rome you could use it for one of the small towns like Siena or Pisa, both a short distance from Firenze.
Allthough you can stay in London for longer than 6 days, with your packed itinerary I would try to take of a day or even 2. Or include a day trip to Oxford within the 6 days.
Your itinerary bypass 2 of the most popular destinations in Europe, Paris and Amsterdam. Any particular reason for that?
When planning your itinerary, try to go south to Italy later rather than sooner. In general, anywhere in Europe is less crowded in September, but in the south you also suffer from the heat. So I would suggest a southbound itinerary. After UK and Ireland, go to Belgium, Germany, Switzerland and finally Italy, and fly back to London. Ryanair has many flights between London and various destinations in Italy. Ryanair can also fly you from Ireland to Brussels to begin your journey on the continent, and you don't need to travel back to Dublin since they also fly from Shannon.
Look out for these cheap flights and if you find one that suits you in price and timing, book as soon as possible. Try to avoid flying on weekends - flights on midweek are normally the best deal.