I'm not saying they were counted but you kept swapping back and forth as to whether or not Lugia and Ho-oh meant something. Even then, two Pokemon, legendary or otherwise, are not enough reason to remake a whole (pretty decently sized) region. They could have easily made them available by normal means in the games, perhaps somewhere deep in the regularly accessible Sevii Islands or something similar.
I'm not talking about a linear connection.
While we likely will be able to transfer from Gen V to Gen VI, no doubt there won't be some huge connection(battling, etc) between the two and this will only make the connection with Hoenn even more tedious than it already is. With Hoenn Pokes being mostly available in the DS era as well, as everyone is using that as relevant, that is only driving the connection to the region itself further away. Going even further, with the GBA slot gone and the DS series to be discontinued altogether in the not too distant future, that will be the final blow to real Hoenn connectivity(and Kanto, once again if you're picky, even though it is available in HGSS).
If that isn't enough for you, not including Kanto(just using it's appearance in HGSS as somewhat relevant in this point) and the 3DS being backwards compatible with DS games, Hoenn is the only region completely inaccessible on the 3DS.
Diamond and Pearl didn't sell some mega amount more though, it looks like they pretty much just picked back up the sales. What exactly contributed to the low sales of RSE(not a real question directed at you)? They were far from bad, something that being the best sellers on the GBA has a right to tell. Is it because of the lost connection from the first 2 gens and making you practically start over? How well do you think sales would have been if that connection was able to be put into place? If the region itself was as bad as people are kidding themselves to make it out to be, how could they make it more appealing? There are plenty of questions to think over.
To go along with , we also have people newer to the series who have never played the originals and would have a go if they were remade in this newer age, as a fresh adventure. Along with everyone wanting to revisit the region in a new light, surely this could be the opportunity to take advantage and make the most of that.
A feature that R/S still hasn't achieved yet. When we get word of the next handheld series in two or so years, then we'll get due report of the remakes, considering they want to risk not making much money seeing as the remakes don't sell as well as the originals and with the already low sales quota of Generation 3, they stand to lose more than gain.
All they had to do was make the two legends available in the games somehow then, perhaps deep somewhere in the Sevii Islands that was actually accessible without an event(even though they were could still be easily obtained if you weren't someone who refused to play spin offs). They sure as hell didn't mind doing that to Groudon and Kyogre. If Johto Pokes were absent for the most part, it would've made sense; Two Pokemon, legendaries or not, is not a real reason to remake two whole (big) games though.
If the whole sales reason is behind why they won't remake the games(using your last statement here), then what exactly is happening in two years that will change that? Nothing. Gen III sales, being long gone, will not magically spring up to others by then enough to change there minds if that is the real reason; They'd still be risking money.