[Klashikari]

I wonder if you did pay attention to what Nagisa became over the course of the past...35 episodes.
She has so many hardship in finally getting graduated for the year she had to do thrice. Not only that, but her efforts were quite limited and she were "literally stuck" in time, as she couldn't go on. (Reference to her question "do you like school", with things that cannot stay the same, back in episode 1).

The whole speech itself has quite a symbolism how she was able to go on, thanks to Tomoya and everyone else. She could enjoy her third grade and finally get herself in society for good.

The whole graduation itself exposes her feelings and has a representation of how her life went. Some people would brush off as it might be just a sheet of paper to receive at a nameless graduation ceremony.
But for Nagisa, it was something she had it quite at heart, despite doing this thrice (and considering the reasons why she failed twice were out of her own responsibility, it adds more bitter and unfair flavor, yet she still face what she has to do, without lamenting or going frustrated over it).

This is the reason why Tomoya prepared such graduation: Nagisa is probably the one who wished to be graduated the most. After so many difficult time, she managed to do that, but fail to have a proper ceremony. A way to express and "reward" her resolve and also enjoy what she couldn't do thrice, with everyone around her.

That is probably one of the most important part of her life, and Tomoya and the rest figured out that much. I fail to see how this graduation was "meaningless", due to the high symbolism shared by all attendants.