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Colosseum and XD were both developed by Genius Sonority, not GameFreak. I think Genius Sonority has somehow retained copyrights to the scenario/plot of these games, so that you don't see any references to these two games in the mainline series because that might entitle GS to royalties of sales of the mainline games.
This goes so far as to include copyright to the Orre region, which is why when traded to the mainline series Pokemon ID fields never reference the Orre region, but instead a "distant land."
Recognizing that you can't reference these plot elements outright, I think the last two generations are nonetheless using them as a design inspiration for characters/plot elements. Anyone who's ever scrubbed trademarked ideas from what originally started as a fanfic/fan tribute is going to recognize this is actually a decent source for creative inspiration.
I think you will never see any outright mention of Colosseum or XD in any future Pokemon game, and they'll probably never get remade without GS's blessing/direct involvement. At the same time, you'll continue to see these games get plundered for design inspiration that aren't necessarily meant to be references for fans, but just a consequence of GF's current team using them for ideas.
I imagine this would make good content for an obnoxious Pokemon Youtube video, but I'm also wondering if anyone else has noticed this. You can easily handwave/dismiss this as plot ideas/design elements shared across video games and anime, but it feels a bit more to me.