Mewtwo: PC/FB offers a middle ground between high-DPS Machamp and high-TDO Metagross against Blissey (and the other Normal tanks, though to a lesser extent). PC/Sh and Cn/Sh remain better for raids, where DPS matters most, but are terrible for gyms.
Rayquaza: Higher neutral DPS, but no SE damage except against other dragons. Sharing a weakness to Fairy with Machamp also holds it back as a generalist gym attacker.
Raikou: Remains a top generalist gym attacker, especially against the common Water-type defendes (its main niche over Metagross as Fire-types are rare on defence).