Considering Hoenn games had the weakest sales of the series, and a well-made entirely new game has possibly more chances of being successful, I don't think it's a given that remakes are profitable.
And don't bring the "GBA was the worst selling Nintendo handheld" card. The GBA was the Nintendo handheld with the shortest lifespan, of course it would sell less than for example the entire Game Boy line, which lasted eleven years, or the DS, counting the DS Phat to the DSi XL, and considering the DSi, despite lacking new games for the 2013 exercise, is still being updated. In fact the 3rd gen games were helped by the fact the old DS still had compatibility with GBA games and by the release of DP a lot of Pokémon were only available via Pal Park.
If you're going the whole region connection route, that can be used for both sides. With the Dsi and onward lacking a GBA slot and the older versions being discontinued, in a way Hoenn(and Kanto, as the stand alone original like you mentioned) have lost their connectivity. That would also keep remakes relevant when you think about it.
Btw, Lugia and Ho-oh were both available in Gen III, remember the Naval Rock event? If not there, you could always trade Ho-oh from Colosseum and Lugia from XD(after purifying the latter) which of course didn't require events. By normal means or not, they were still available.
The idea was to catch them on the DS only, not to mention the version mascots were never officially available in the handheld series apart from events which couldn't even be widely distributed because the GBA didn't have access to the internet. Meanwhile, Groudon/Kyogre/Rayquaza could be caught in HGSS and sent to BW.
So far there are two instances in the series where you need cross-gen trading to acquire all the Pokémon: from RBY to GSC (since GSC didn't have the RBY legends), and from DPPtHGSS to BW. The difference is that they're all within the same generation of console. They wouldn't support the GBA forever, because the GBA carts are huge compared to the DS and they could easily make all GBA games available in Virtual Console, so it was needed to make all Pokémon accessible within the DS only. And Hoenn fans who own only a DS can't complain, as the games feature most of the Hoenn Pokémon if not all of them (I think only Jirachi and Deoxys must be acquired through events).
Johto was a neglected region in the 3rd gen. You couldn't access most Pokémon without owning a Gamecube and having the console games. Only Emerald gave you the possibility of acquiring a Johto starter in the handheld series. Whereas in the DS, the Hoenn starters could be acquired in HGSS with no major requirement, and all starters are available in 5th gen through Dream World events.