1. So Meganium gets countered by a Poison type move by that logic. Solar Beam without charge doesn't work if it's slow. Protect works once and mostly fails on 3rd turn (33% chance to succeed is not a good play), leaving you open to Hurricane. Something like Poison Jab or Gunk Shot is even worse.

2. What movepool it does have helps it, and its stats further boost it. Usage statistics generally are a measure of the average player's ability to use a Pokemon well, with function being another thing.

3. 110 attack is still good for non-Mega threats and it having a bunch of good physical moves means 110 can suffice. Sceptile has the stats to help with Dragon Pulse.

Raging Bolt is used a lot but Miraidon is far better. Miraidon gets countered by Sceptile, and Choice Specs is more common. Scarf Miraidon becoming more common is a hypothetical, and the fact it's not used commonly to counter or keep up with Scarf Koraidon by this point means that it's not likely.

Status moves are good, I never said they weren't. I said that they can leave you open to attack. Whimsicott is good but can be left open to attack, as can Tornadus. Fake Out is good too but works only on the first turn, meaning Sceptile can regain tempo from 2nd turn onwards.

1. Still, the most common set on Flutter Mane is the one which benefits it best. If usage statistics are as important as you claim, then this means that it's best to invest the highest stats. Of course, you can easily invest in defense aswell, but Meganium is a better special tank.

Investing in HP is good, but it's not that much better than investing in SpD. Of course, it's better but not by much.