Well it could easily be a hint towards potential remakes. I mean the Rocket grunt was there because they wanted to show the player that he was from Unova, and it was a fun little reference. The fact that he was replaced by Team Aqua/Magma grunts who were married is... well, it's SOMETHING (I'm not sure if they're actually married or whatever, but that's what I'd read somewhere).
I'm hopeful that there will be remakes, although I'm curious as to how they could be executed. For one thing, B2W2 have pushed the timeline along another two years, and the general consensus is that about 5 years (give or take) passed between the 4th gen games and the 5th gen games. Which would mean that B2W2 took place about 7ish years after RSE/FRLG (which are believed to take place in the same timeline).
B2W2 spoiler coming here, so be careful!