Eh, I guess I don't really disagree enough with you to make a long post about it, but I do think that a bunch of decisions for a while were influenced purely by toy stuff. I know it's a commercial, and that its purpose is to sell toys, but I still think that it's better for a company to let the creative people do their thing and not shoehorn in things like Twilight's giant-ass castle just to sell playsets. But then, that's what the show always did pre-FiM, and it was wildly successful then.
So really, it just comes down to a question of whether it's okay for companies to squeeze maximum profits out of something simply because they own it. Obviously, since the companies own it, they're entitled to do so - but I'd still argue that criticizing them for doing so when it hurts the property is justified. If I somehow owned an original Picasso and decided to burn it, that'd be entirely within my right, but it'd still be a stupid thing to do.