There's one connection most people aren't making regarding a university's status as a "research" institution. Just like the label "Christian," which, according to most Christians, doesn't apply to members of the Church of Jesus Christ of Latter-day Saints, a "Research Institution" isn't named such for the actual quantity and quality of research done, but for who does it, how it's used, what it's for and how it's financed. It's just not being done OUR WAY (sound similar to the "christian" arguments???).
It's no secret that BYU's emphasis is on Undergraduate education. Yes, we have many and great graduate, doctural and JD programs, but that's not the reason BYU's there (as an aside, I still say one of the biggest reasons is getting a lot of worthy little Mormon boys in the same place as a lot of worthy little Mormon girls, and I don't have a problem in the world with that. Maybe it's the biggest reason, maybe not, but if it's up there, it also helps explain why undergrad is more important than grad work. If you're not going to get married in the 4 (5.5? :whistle: ) years it takes you to get your Bachelors, you're less likely to it in the 2 years it takes for your Masters either).
Regardless the reasons though, BYU has poured the lion's share of its resources into getting students an undergraduate degree, when they know that's not where a University's prestige.
I don't have the particulars on all the data that goes into ranking a school on the Research scale, but I do know that it's much more involved than just the number of graduate or doctoral programs offered, or the percentage of the students getting those degrees. A heavy hitter is the amount of Grant mony is awarded the school, and most of that money comes directly from the Federal Government. BYU also makes no secret of the fact that they're very selective about what money they take from the Gov't, because of those pesky little strings that manage to attach themselves to the money. BYU simply doesn't get its research funding from places that are counted by said rankings.
Thoroughly UNDER-represented in the calculations is, oh, the ACTUAL research being done. BYU, contrary to most peoples' assumptions, is a HUGE and well-respected research institution, with tens of millions that go towards it every year. For a school without a Med Program and Hospital (calculatedly so, by the way, for those who are annoyed at the Church for that, much less liability and overhead. Whaddaya need for a business and law program? Two buildings and two staffs, and books. Whaddaya need for a Med School? A bleeding (forgive the pun) lot of technology, instruments, insurance out the wazoo, oh, and an entire HOSPITAL. Not gonna happen. Doesn't need to), that's quite a lot. So if BYU is doing a lot of research, but it's not all being done by Grad- and Doctoral Students, who's doing it???
People just assume that any undergraduate education is a cookie cutter match of any other, or at least treat them that way, and that an undergrad from BYU is the exact same as an undergrad at any other school known for its "research." In my experience, there is a HUGE difference. For example, people may or may not know much about the donations Ira and MaryLou Fulton have given the Engineering Schools and what the money went to. We're talking about literally HUNDREDS of millions of dollars here, and it has gone towards cutting edge software and machinery and technologies, the likes of which are found at few other Universities. The MAJOR difference between us and them is that at other schools those technologies are being accessed by Doctors and Doctoral Students exclusively, and at BYU, undergrads like me had access to them. I didn't really realize at the time why all my professors were raving about it, but literally ALL of them were telling my classes that NOBODY had access to the types of technologies we had access to unless they had a certain 3 letters following their name. It was simply without precident. We worked directly with our professors on their research. Now, this isn't to say that my education was necessarily BETTER than anyone else's, but I have found in the last few years in the industry that friends with undergrads from other schools universally had professors who treated their students like it was beneath them to be there and that they had better things to be doing, and had minimal technology available to them.
Interesting to me that BYU doesn't focus on the exclusivity of the system, but more than holds its own in terms of results. More and more, the Pac-10's Academics complaint is looking like another invalid excuse, and even though it could be considered a disadvantage for sports, I'm kind of proud that we don't make our University's emphasis worshiping in Nibley's "robes of a false priesthood" like others do. ;)