You're conflating what's good in competitive with what's intended to be good, when a lot of Pokemon that Game Freak probably intended to be relevant aren't, and I assume that's because they don't understand what actually makes something usable in the main series. Also, it sounds to me like you're referring to OU, but you never acknowledge how that's an unofficial player cultivated metagame that probably isn't what Game Freak intended anyway.

At least in the main series there are Pokemon who can get around their low stat totals with other advantages, for example Breloom who's been consistently strong despite having terrible stats.

I think we've already seen that using the main series games as a model of how things ought to be isn't the best way forward, Niantic have departed from the main series egg hatching ranges for example. If people could use their favourites, even if it required a disproportionately large stardust and candy investment, the game would be more diverse and more interesting, and if it did require disproportionate investment then there would still be good and bad Pokemon as intended. But people would have choice.