Maybe its just my area, but I'm hard-pressed to think of a single paper I've come across by an Alliant grad (and only very rarely by their faculty members, for that matter), whereas I can think of several from Pepperdine. Though yes, that is anecdotal.
I wouldn't look at the raw numbers though as that isn't informative - the Alliant system is pumping out several times the number of students that Pepperdine does. The broader point is that if someone is planning to have research be a significant part of their career...we are at a "lesser of two evils" scenario. Neither is known for research, neither has a great track record for producing academics (even clinically-focused ones), and they both had very weak records in terms of grants/pubs last I checked (with perhaps the occasional exceptional faculty member they brought in from elsewhere). Regardless of which institution you are looking at, its pretty clear that one is going to have to go above and beyond to try and get decent research training at either of these institutions.
Of course, I also think if one is planning on a research career, one should do everything possible not to have "Alliant" or "Argosy" on one's CV.
