Hate to say it, but that's basically what I was expecting, just wanted to make sure there wasn't some dark secret interaction reason otherwise. It just seems like these days nobody ever uses Agility, I honestly thought they might have just forgotten it existed.
The reason why you haven't been seeing Agility/ Rock Polish Metagross as much is not because of the fact that it has two moves that give it +2 speed but rather because the Pokemon itself is used almost exclusively as a 4-attacks Pokemon rather than a late-game cleaner. The metagame has really adapted to Metagross, with things like M-Scizor and Tank Garchomp being prominent in the meta right now. For this reason, the extra moveslot is generally better used for a fourth attack instead of a setup move. In short, metagame trends have made M-Metagross, especially Agiligross, less viable, which is why you see it less often.