It's very formal, but your English is very good. There are only a few minor points.

Formal letter about a trip

That's a very common spelling error even for native speakers.
First of all, we couldn't reach Ostia as the bus broke down soon after our departure and I it had never been replaced.

Most likely "I" instead of "it" was just a typo.

However I would recommend saying "It was not replaced" rather than "It had never been replaced". In this case you are not talking about whether the bus had been replaced at some point in its lifetime, but whether is was replaced when it broke down on that specific trip.

Secondly, I was surprised by the fact we were supposed to pay for the entrance fees to the monument,; that had not been mentioned before.

A couple of very minor points; you normally pay an entrance fee, you don't pay for it. An entrance fee isn't what you are buying; the right to enter is. You would therefore say either "supposed to pay the entrance fee" or, as an alternative, "supposed to pay for entry to".

Also, I would use a semi-colon, not a comma. A semi-colon is used when you have two clauses that are largely independent, but you aren't joining them with a conjunction. What I mean by that is that "that had not been mentioned before" would work as an independent sentence. (And indeed it could be.) A comma is normally used if the clauses cannot stand alone, and are part of the same "thought", for want of a better term. (This is a general rule, not an absolute one.)

As a result of my experience, I would like to make some recommandations recommendations for future tours.
It would be appreciated if you arranged would arrange for alternatives in case of bus breakdowns or other unexpected events that may occurred.

You are talking about something that MAY happen (conditizionale) in the future. However while "if you arranged" is sometimes used to refer to the future, it's really an expression of the past. More importantly it isn't conditional. The arrangement would only apply IF such an event occurs. It's therefore better to use the conditional "would". "Occurred" is definitely past tense; it needs to be "occur".

Furthermore, it seems only fair that you should make more explicit the fees that are not included in the offers, and I suggest that you to improve the guidebooks you provide to customers, as their low quality didn't allow us to totally enjoy our journey and the city of Rome.

Nicely done.