On that note, it should be noted that Thrifty participates in KU and QF while Dollar doesn't, and Dollar participates in NH, JL, and (as Mrp Alert mentioned) VS while Thrifty doesn't.

But yes, all other things being equal, I'd pick Thrifty over Dollar.

(Another benefit of Thrifty: Dollar has historically been airport market-centric whereas Thrifty has tried to penetrate the local market a bit more in the past, meaning there are more Thrifty locations in cities and in smaller towns than there are Dollar locations. This opens up the potential for extra assistance if you happen to be near one of these locations, although if they're franchised [which most of them are], there won't be much they can actually do for you beyond perhaps helping out of their own good will, since they don't have access to anything special beyond the phone numbers, etc., already provided to you.)