Even if you doesnt want to visit Milan anymore but may you start there
Milan - Genoa - Cinque Terre - LaSpezia (Pisa) - Rome - Naples - Sicily (Island) - Tarrent/ Lecce - Bari - Florence - Verona - Milan
This is a difficult question, but assuming you want to cover as much as possible you need to concentrate on the mainlines, which excludes many of the minor branch lines and of course the smaller towns and villages.
A check of the main lines shows a relatively simple network.
Across the North from Ventimiglia to Genoa to Milan (also Turin) and then Bologna, Verona and Venice
(Then north to Trieste).
Then there is a high speed line from Bologna to Florence to Rome to Naples and ends at Salerno.
From Rome/Salerno there is the coastal line down to Vila san Giovanni and Reggia Calabria. Fron V S G you can stay on the IC service from Rome to across the Messina straits Boat train and on to Palermo or Syracuse.
From Rome you can then cross to Bari etc on the East Coast,
There is also a route down the west coast from Genoa to Rome, which can be linked to Pisa.
All these routes operate both Freccia (high speed trains) and Intercities trains (Only ICs in Sicily).
The high speed lines tend to only operate to the main cities, whilst ICs stop more often and servw many smaller towns.
Seeing ´tutte ITalia´ is not possible for anyone. You have to restrict yourself-you also did not give a clue to how much time you have in total. Neither on WHAT interests you most-this may lead to quite different routings. Some go to visit as many roman-catholic religious places, some to visit old-Roman ruins, some to taste as many types of penne/spaghetti as this country has, etc.
The hi-speed rail network is in basic a T-Torino-Milano-Venezia (incomplete stll) with the old line MIlano-Roma-Napoli off it. The old-style network with faster IC-treni is basically the lines along both coasts-this also still has a few treni notte=overnite left.
For 1st timer it seems to me a variety is best: so either Bari OR Lecce, Pisa is a short stopover if you come off Firenze (there is hardly anything else as that tower), now decide if you want beach/seaside or not in heated summer.
For those in trasportazione: IT has 14 cities with Tramvia and 14/15 (many do not run in summer) with filobus=trolleybus, a bus under electric wires. This may bring you to cities you never have heard of.
