I do find it very interesting that a company such as Game Freak is this rushed and hard-pressed for ideas; at the same time though it isn't very surprising - there's a new main Pokémon game literally every 12-18 months; never mind all the spin-offs that come with it and I guess smash every once in a while. This interview to me just solidifies the idea that Game Freak needs to calm tf down with the releases and put quality before quantity.
Though, on the note of fan-submitted ideas... I think that could be very interesting. I remember back in 2002-2006 or something like that, one of Lego's lines Bionicle which I was very into had a lot of fan-submitted creations used and canonized, and I mean a lot. Local wildlife, the bulk of an international bounty hunter syndicate, a ton of weapons, the designs for a lot of important characters... it worked out extremely well for them and that level of fan interaction was I felt honestly one of the big strengths for Bionicle at the time. That said, I'm not entirely sure how well it'd translate to Pokémon considering Lego is based around the consumer's creativity and the fact that Pokémon is far, far more popular than Bionicle ever was or will be, but I think some kind of fan interaction of this kind would be a welcome addition.
... I just completely derailed the thread. Whoooops.
Also Gen VI is also the generation that GameFreak jumped to the third dimension. Everything (aside from menu sprites) had to be given a model which would take up a lot of time. "But the team who came up with Pokemon designs have nothing to do with the 3D modeling." The 3d modellers would need to know a Pokemon's proportions so I imagine the designers spent a bit of time on that. And that's not mentioning designing characters and environments (I assume its all one big design team, like they may have people who specialize in certain areas but I would think for the most part they would work on all parts of design in the game).
But that was Bionicle in its early days. As I said, with all the fanmade Pokemon stuff out there the possibility of someone stealing someone else's idea is possible and could be difficult to verify. Even if they say you won't get anything for your design being selected they would probably still require they have all rights to the image and if this is done without the original image creator's content it would cause some problems. While I'm not saying GameFreak can't take design inspiration from other's work, they can't really pick one and make it into a Pokemon or lift aspects right off multiple people's work and cobble it together.
That's the magic of Mega Evolutions, though. Holding a Mega Stone - and Mega Evolving - is considered an option for a Pokémon, rather than being the "end of the line" as a normal evolution chain implies. A Pokémon may only evolve once, into a design it's permanently stuck with, but Mega Evolution is both optional and temporary. No matter what kind of a Mega Evolution Flygon would get, we'd still have regular Flygon as the end of Trapinch's evolution line, and Flygon's existing design would be on display in every occasion other than in certain battles under certain conditions.
Moreover, Game Freak has already made presedence for giving one Pokémon multiple Mega Evolutions. Both Charizard and Mewtwo have two Mega Stones, which will temporarily turn them into different creatures. There is literally no reason why Game Freak shouldn't give this option to more Pokémon. If they made a Mega Flygon they were not happy with, they could simply add another Flygonite.
As for the last bit... Well, I'm unsure if new Megas could be made for this generation. I've got a sneaking suspicion that creature design for the entirety of Gen. VI was done during XY's development, and that Game Freak have already finalized their pool of Mega Evolutions. If they were unable to make Flygon before ORAS, they might not have been able to make it for Gen. VI at all. Then again, I could be wrong, and they could have sat down and made one after the responses they got after ORAS' release.
At any rate, it's pretty certain that the next games, whenever they come, will contain more Mega Evolutions. Game Freak are probably hiding some fan favourites "up their sleeves" to satiate our desires to see old fan favourites brought into the limelight. Even if Flygon is not among them for the time being, I bet we'll enjoy what's coming anyway.
I'd even argue if they were able to remove anything about a Pokemon, it would be a Mega Evolution. They don't like something about a Mega Evolution and have an idea for a better one? I don't see why next gen they can't change/replace it. Sure, they could make it an additional Mega Evolution and probably should if it plays differently from the current Mega Evolution; but if they want to make a better version of the current Mega Evolution I don't see why they couldn't replace it.
And I think by now they would probably have prototype ideas/designs for all Pokemon who would be capable of Mega Evolving (or at least close to all the Pokemon), all they need to do is just pick the ones they feel like they want to work on and finish it (or come up with a completely different Mega Evo they had thought of if they get a flash of inspiration). And I'm sure they have some fan favorites close to or already done but held back upon, just like they hold back certain kinds of animals or things that can be made into Pokemon (it took them 6 gens to make a T-Rex Pokemon, and we still don't have a dolphin Pokemon). We might have to wait till next gen for Mega Flygon though if they're having a hard time coming up with a design, unless they have already gotten over that hurdle after the release of ORAS (sort of like after completing a test you finally remember the answer to that question you know you should know but can't remember).
I don't know if anyone can buy the idea that they just couldn't come up with a design, considering a lot of megas have pretty uninspired designs. They have some pretty common trends in their mega designs that they could've used here, like changing the wings up a bit, adding a whole bunch of spikes, stretching out the mouth, messing with the antennae, changing up the color scheme, etc. It would not be that difficult, although I can't think of a better reason why they didn't.
While there are Pokemon who are pretty much just an advance looking version of their normal form, to me it looks like at least for the ORAS Mega Evos they wanted to try something different by focusing on a certain theme for that Pokemon.
For Beedrill it's its needles (its legs turned into needles, the needles it already had got longer and more pronounced, its body was shaped in the way that the needles were right in front and prominent)
Slowbro it's its Shellder partner (the Shellder had completely covered its body creating a sort of armor)
Sableye it's it jewel (it had popped out and grew to become a shield for Sableye to hide behind)
Salamence it wanting to fly (its shape changed to look a bit more like a glider)
The Eon Duo its them looking like jet planes (their arms turning into turbine/rocket-looking attachments and getting spoiler like appendages on their underside)
Lopunny they made into a martial arts fighter (ears turning into nun-chucks and its legs looking like ripped tights)
Gallade turned from a gladiator into a heroic knight (its body becomes more white and it gains a cape, its blade arms look even more like blades)
Audino it's it medic aspects (it gains a stethoscope crest and its fur now looks like a doctor's coat)
Diancie it's it being a queen (its body changes to a full dress including a veil)
Considering how popular Flygon is I think they wanted to do something special with it besides making it Flygon+. But they couldn't figure out what they could focus on with it.
Would they still use Aarune though? Hoenn's edge for Secret Bases had to do with the exploration and dotting them all over the region. In Sinnoh, they felt much more separate because they were all in the Underground, which in itself was kind of a side activity akin to Gen 5's Dream World.
Flygon can learn Dig. If they want to use Aarune as the mascot for the Secret Bases I don't see why they can't bring him back. Like he came to Sinnoh to spread the idea for Super Secret Bases, discovered there really wasn't much places for them but then discovered the Sinnoh Underground and thought that would be the perfect place to set up Secret Bases. He could work with the Underground Man (who I just found out was Byron's father and Roark's grandfather) and be the one to give the player the Digger Drill.