I'd say this is far from ideal. First, Sceptile's type isn't the greatest offensively. We should keep in mind there are far more types resisting Grass and Dragon than types hit super-effectively, which means Sceptile will more often than not have to fall back on coverage moves. To make things worse, Sceptile's ofenses are average for OU, so if GF try to boost them both, Mega Sceptile (which can't use a LO like its base form) might end up having a lower damage outpot than regular Sceptile. And that's awful for a mega!
Also, since Sceptile lacks a consistent way of boosting its Sp.Atk and even at 145 Sp.Atk (which sadly is a best case scenario) won't have an extraordinary damage output, I'd say it's more of a hit-and-runner (trying to grab a Lightning Rod boost or hurt things with Leaf Storm) or late game cleaner. It probably won't be a main sweeper or wall breaker. So let me argue that instead of an Atk boost over even a huge speed boost, it just needs as much bulk as necessary so it can afford a mispredict on the switch. Just give it +5 Speed so it'll outspeed Greninja and every other Dragon in the game. +11~20 would be nice for outspeed Jolteon/Mega Manectric and being able to force them out after absorbing an electric move, but that's too specific. I'd personally give it +5 so it can get as bulky as possible. Having 145 Sp.Atk/125 Speed would leave 55 points for defenses, potentially turning Mega Sceptile into a specially based Garchomp - a fast and powerful sweeper with the ability to survive a powerful hit as long as it's not super effective. And it would still be outclassed offensively by Garchomp because of its worse STAB and lack of LO/set-up move.
But of course GF won't do that. They'll probably overinvest in Speed and dump some points in Atk, possibly giving it a Sp.Atk lower than 145 and a mere +10~15 on defenses. That way Sceptile will remain frail and hitting decently at best (but above the average for OU). In other words, rather mediocre :/
I don't quite agree with that. Okay, Rayquaza doesn't share a commom origin with Groudon and Kyogre, but they're still a trio that should be given equal treatment. They have an in-game link (Rayquaza stopping Groudon and Kyogre in Emerald) and an external link (they're third Gen main game's box legendaries). It's like the starter trio: they have no relationship according to the lore but they belong together nevertheless. Just think at how everybody reacted when only Blaziken got a Mega Evolution. Or how weird it would be if Mawile were given a mega evolution and Sableye a regular evolution. I agree it won't be crazy and random if they come up with a new story and Rayquaza ends up as the only member of the weather trio to get a mega evolution and not a primal devolution, but it still won't feel right.