¿Qué significa Es war aber sehr schön, Sie heute zu sehen. ?

See a translation

1) depends on the type of "meet"

meet up/ see someone again (for example visiting a long time business partner):
"sehen" is fine

meet someone for the first time: "kennenlernen"
careful: "kennenlernen" is one of the words that "eats" the "zu":
"Es war sehr schön sie heute kennenzulernen."
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2) I would also drop the "aber", unless the context demands it.
Which is only the case if the sentence before mentions something bad/negative.

"Das Wetter war schlecht. Es war aber sehr schön, Sie zu sehen."
("The weather was bad. BUT it was very nice to meet you.")

If you ended on a positive note, the "aber" is not necessary:

"Das Essen was köstlich. Und es war schön, Sie zu sehen."
("The meal was delicious. And it was nice to meet you.")
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3) Do you know when to use honorifics ("Sie" vs "du/dich")?

If you use "Sie" with friends it can be seen as cold/distanced.

As a rule of thumb:
- use "du/dir/dich" ....
...if you call someone by their first name
.... at parties/ clubs
...with other students at university
...if it is a private setting (example: you visit your sister and she introduces you to a friend of her that is also there)

- use "Sie/Ihnen" ...
...if you use the last name
...when talking to customers or staff
...in official/business settings
...when talking to strangers in public*

*Younger generations (which includes people up to ~30) are usually fine with not using honorifics.

In general I would say it is less strict than keigo vs tamego.