Yep, do you know how many player have thought of some connection when they have played Final Fantasy VIII for the first time back then? That's why nobody knows who initially started the idea of R=U due to the open-interpretation design and that's why Square doesn't want to spoil us (for example, not showing the whole world more details about the plot). The Ultimania Guide is merely an art book consisting of in-depth explanations about the FF8 magic, it's history, sorceresses, interviewers' talks and other misc stuff, that's all.
Actually, in my experience very few actually thought of R=U just after playing the game. Many are confused at Griever's appearance in the final battle, but rarely do they make the leap to R=U. Whenever I've seen new people claim to have thought of it themselves it's been blatantly obvious they were copying stuff they read on other websites.

But anyway, that's moot. I don't see how you can dismiss the Ultimania calling it "merely" a book consisting of in-depth explanations on many plot points, when that's entirely relevant to R=U. In addition, the Ultimania actually does give clear allusions to Ultimecia's background, so clearly one point of the guide was to help clarify Ultimecia's motives. And well, those allusions aren't towards R=U in the slightest.

In fact, not only does the Ultimania not mention the theory at all and rather allude to another idea, they actually also provide a crushing argument against the theory (the human lifespan fact). When you take into account that the game itself backs up very firmly what the Ultimania alludes to in a natural way (i.e. through all of Ultimecia's dialogue), R=U has only got a collection of vague hints, all of which can be interpreted naturally in other ways, none of which are remotely strong enough to make the theory plausible.

Put all that together and I think it's pretty clear that in the end, Square didn't intend R=U. At best they were considering it and one point but decided to drop it, leaving a couple of the vaguer hints. But let's face it; Final Fantasy is, besides FF7, not known for villains hidden in as much obscurity as R=U requires. And for FF7, they explained most of the details in the FF7 Ultimania anyway.