On the one hand, 5D's was far better handled than its predecessor (because seriously, GX, what the heck?!), eventually using its own take on the Yu-Gi-Oh! world to create a story that is fairly unique and its own, and also is completely daft in a lovable way.
On the other hand, perhaps it's better that it's being retired while it's going well, because it looks like the developers are having terrible ideas again. (I'll hold judgment on "Yu-Gi-Oh! ZeXal [pronounced 'zeal' for no good reason]" until I actually see for myself that it's completely terrible, but it isn't promising.)
I'll still be sad to see it go.
Actually, there's an undercurrent that's been going on as the series has progressed where it seems that the opening and ending sequences have developed a slight disconnect, wherein it seems that Yusei's and Aki's relationship is developing at a slightly different pace than in the series itself.
I'll note that, while I am a dude and thus not much for "shipping" (unlike about a bazillion percent of this fandom), I totally ship Yusei and Aki like heck. But I'm not going to pretend that their relationship in the series even begins to parallel what we see, in the endings particularly.
And to show that I'm paying more attention to these things than is really sane or healthy, I'm going to go through each of the 5D's Japanese series openings and end credits, and list the correct sequences that the characters appear in, in the name of seeing the development of their relationship via spacial arrangements.
In the first opening, the order is Yusei, Jack, Aki, the twins, and Rex Goodwin. In the corresponding ending, only Yusei and Jack appear.
In the second opening, the order is Yusei, Jack (with Carly briefly), Aki, the twins, Crow, Misty and Carly, Kiryu/Kalin, and then Yusei again. In the corresponding ending, we can see Yusei on what used to be the Junkpile of Solitude in the first opening, now crowded with a huge number of people, the closest of which are Jack and Aki. The character order is Yusei, Jack, the twins, Aki, Crow, and then Jack, Aki, the twins, and Yusei again. There's a second character cluster after this that has Aki and Jack a nearly equal distance from Yusei (though Jack is closer, the image is slightly misleading because the characters are of such disparate heights and standing on different levels).
The third opening plays with Yusei, Jack, and Crow as the Three Musketeers/Caballeros/whatever. Character order is Yusei, Jack, Crow, Aki, and the twins (plus a gaggle of those schoolmates who haven't been seen in ages), followed by Dark Glass/Vizor/Bruno and Sherry disguised as a dude (though this was one of the openings that changed over time, and I'm looking at the first version).
Here's where things start getting more interesting. Observe the following screenshot.

And here's the last bit of this particular opening sequence:

In the third ending, the first character order is Yusei, Jack, Crow, Aki, and the twins. Then comes Jack, the twins, Crow, Aki, and Yusei... and it's in this Brady Bunch style box, with Aki next to Yusei.

Somewhere in there (I think) is this still image-while the focus is on Jack and Crow, look at Yusei and Aki in back there.

The fourth opening doesn't have any of those slideshows or such weirdness-instead, it has a sequence which pays attention to normal motion and the laws of physics. (Go figure.) It should be noted that Aki's sexy biker suit makes its first appearance in an opening here.

There's also this brief sequence where we see them walking in line, and Aki is standing in front of Yusei.


And here she is, ensuring that Bruno/Dark Glass/Vizor/Antinomymony keeps away from Yusei.

The fifth ending finally has figured out how to be internally consistent, because it features the same order-Yusei, Jack, Crow, Aki, and the twins-twice... even though this is the "wheeler order" sequence, where it'd have made more sense to have it be Jack, Crow, Yusei, Aki, and the twins.
Then comes this crowning indicator of where their relationship apparently is in ending land:

It looks like a pretty serious relationship at this point.
Chances are, there won't really be any more new Japanese 5D's openings or endings (unless maybe the final ending is like what they did for the Duel Monsters series), but perhaps it's for the best. Imagine where it would go from here if one takes into account the fact that apparently their relationship moves faster than in the series itself.
Imaginary ending six still, courtesy of GDG (and with a greyscaled screenshot in the background):


And the still from an imaginary eighth ending:

...
No, now that I think about it, I want to see that after all.
#@%& it, Konami!
-Si