Doing research, outside of my specific interests, for a MS program Here's a very brief description of my scenario: I have ambitions to pursue a PhD in a bit a of fringe field (vertebrate paleontology). I already have schools and faculty in mind who are doing research I am very interested in. But I find it very important to first get a MS in order to secure research experience and to possibly offset my less-than-immaculate undergrad GPA. However, the schools I'm set on for a PhD do not offer MS programs.

I am currently in the process of applying to 6 other schools for a MS, through departments of biology, zoology, and geology (My undergrad was in Bio). Only 2 of the schools contain faculty members whose interests are at least decently aligned with my specific interests. But I don't want to limit myself, so I'm applying to the other schools as well, even though their faculty members' interests may not be too relevant to my specific interests.

So what my question boils down to this: In the event the other 2 schools don't work out for me, would it be worth it to temporarily change my desired research interests to better align myself for a MS program that is at least in the same discipline?

Like I mentioned earlier, my main reasons for wanting to enroll in a MS program is to gain experience in research, and show that I can perform well at a graduate level. So my initial thought is "Yes, it is worth it". But I am also concerned about unforeseen consequences this may have. Is it common for someone to change their research interests between switching from a MS program to a PhD program? Or are there complications with that I may not be seeing, and I should stick to applying to schools that better suit my current interests?
You shouldn't say that you want to do something you're not interested in just to gain admission. It will end badly for everyone.

If you're just not certain you're going to like an area, that's a different story. There are a lot of programs where you have the ability to be "matched" with an advisor before or after admission. In such cases, the key is to finding a match you're happy with.

But if you're asking if you need to change research focuses as an undergraduate to align with programs later, the answer is that you don't. It's understood that people are likely to change issues early on. (After all, faculty members do so regularly; why can't students do so before joining their group?)