Can't believe I missed eight pages of this. Not quite as much as I can't believe it happened at all, though. Maybe I shouldn't be surprised anymore.
I'll be perfectly honest I think the flowers are a clear reference to Aeris. I mean with the white materia, although it belonged to her, there's enough leg room to say it's something associated with the world and that's cool but
The flowers have always been used to indicate her presence in Advent Children -- isn't there a specific scene showing her flowers with Zack's sword as a little memorial to their memory? and then the flowers in front of the family photo as a nice little reminder that she's still their family even though she's dead.
There's good points to be made there, yeah.
I myself see the flowerfield at the end as only peripherally an Aerith reference. Here's why:
Even the Ultimania for Dissidia tells us that Cloud's still regretting the deaths of Aerith and Zack in Dissidia, so it clearly took place for him between the events of the original game and the events of AC/C.
Ever since Case of Tifa and AC, I figured that Cloud's line at the end of the original game about wanting to meet Aerith was because he wanted to get her forgiveness. In Case of Tifa, that same night he said that line, he's also saying he has to survive because he'll never be forgiven otherwise.
So, he's already associated Aerith with guilt/forgiveness at that point.
Then we get the line in Dissidia about the one he really wants to meet -- at a time we've been told he's still feeling guilty. And he's standing in the Northern Crater, looking up, just like the last time he said something like this.
See where I'm going with this?
A flowerfield is where Cloud eventually asks Aerith for forgiveness, he and Firion speak of sharing one another's dream in Dissidia (a dream related to flowers), and then Cloud departs into a flowerfield at the end?
Seems to me that, where Cloud is concerned, flowers are a symbol of redemption. And, yeah, that is related to Aerith. Not in any kind of romantic way (put down the pitchforks), but, sure, it's related. Inarguably.
So I wouldn't call the flowers in Dissidia an Aerith reference per se, but a redemption reference.
Looking at Cloud's arc from the original game to AC/C, it makes sense. It's really only when you try looking at Dissidia as self-contained with him that things get a little muddy.
While you would do that with most of the characters in the game, I don't think you would do it with him given that -- unlike the others -- a very specific timeframe was applied to Cloud (when he was still feeling guilty) for Dissidia, with Advent Children Complete coming out only four months later.