Gonna answer it myself. Why few other Pokemon use sub and agility? Well, because there's no need for them too.
Let's list some Pokemon for some examples, then I'll explain the general theme.
For use in OU and UU (the highest tier with a banlist and the tier with Empoleon in it), I count maybe 20-24 arguably viable Pokemon. Here are the noteworthy ones.
(Mega) Beedrill: Doesn't run because it's very fast already, and needs what coverage it gets. It also makes good use of U-Turn which counteracts speed boosts.
(Mega) Pidgeot: Already fast and doesn't need a speed boost. Also needs what little coverage and STABs it gets.
Arcanine: Has awesome coverage including healing moves and extreme speed. It really doesn't need a sub or a boost because you just send it in and spam flare blitz 80% of the time anyway. I.e it's redundant.
(Mega) Aerodactyl: Extremely fast and has multiple sets it can run normally that cover many bases. Agility set is pretty redundant.
Zapdos: Although some Zapdos do actually run Agility, it's rare and almost never simultaneously with Sub due to it needing coverage/healing to be used effectively afterwards. Plus most are defensive anyway now. I.e either doesn't fit or redundant.
Dragonite: Has access to Dragon Dance and Multiscale, completely outclassing Sub+Agility.
(Mega) Scizor: Best move is arguably Bullet Punch, which makes Agility redundant. Also has great coverage and support moves it doesn't want to give up.
(Mega)Metagross: Already has 4MSS, taking two of those away makes it extremely hard to break past important threats.
There are more you can look up with the moveset calculator, but you get the jist.
1.) Pokemon are either reliant on their coverage moves to function adequately against common or important threats to give up two moves or possibly even lose their niche. They may have to use certain moves or tactics in order to actually stay viable. 2.) Pokemon have other sets that simply outclass the Agility set, making the set arguably worse or again sacrificing the whole point of using the Pokemon. 3.) The Pokemon is generally unviable in the current climate, with the set impacting their ability to fight common threats or the Pokemon is simply not as usable. 4.) The Pokemon in viable but either needs significant support or entire teams based around it, making them more trouble than it's worth.