TL;DR. Two coastal airline cobrands at similar prices. JetBlue Plus ($99) earns 6x on JetBlue, 2x dining and groceries, 1x other, plus 5,000 anniversary points and a 10% redemption rebate. Atmos Ascent ($95) earns 3x on Alaska and Hawaiian, 2x on six broad categories, plus the Companion Fare. Pick based on which carrier you fly: JetBlue (East Coast leisure) or Alaska (West Coast and Hawaii).
The three dimensions that actually decide it. First, route network. JetBlue is strong NYC-Florida and NYC-LAX. Alaska is strong West Coast and Hawaii. Almost no route overlap. Second, anniversary benefit. JetBlue's 5,000 points (~$65 in value). Alaska's Companion Fare ($99 + taxes for a paid ticket companion, worth $200-500). Companion Fare is the bigger anniversary perk. Third, fee. Within $4 of each other; essentially tied.
Real customer scenario for each. If you fly JetBlue from JFK to Florida 4+ times a year, JetBlue Plus's 10% redemption rebate keeps your TrueBlue compounding and the 5k anniversary points cover most of the fee. If instead you fly Alaska from Seattle, Atmos Ascent's Companion Fare is the more valuable anniversary benefit by a wide margin.
The trap to avoid. Picking based on signup bonus alone. Both bonuses are temporarily inflated and route applicability matters far more than the welcome offer over a 5-year hold.