I used to be much more of a LEGO purist, the farthest I'd go was to switch out the "arm" pieces on torsos, and nothing more. However I've changed, as many people do, since I first started brickfilming.
Restricting yourself to just one brand is not allowing yourself access to the potential that the other sets/brands can offer you. For instance, I've always wanted to make an original Sci-Fi brickfilm, love Johnny Thunder and Egyptian sets, and, as I'm a bit of a fan of the Stargate series, I decided to buy a "Best-Lock" SG:1 spaceship set. Sure, the pieces are of the same quality of disposable army-men, and nowhere near the quality of LEGO products, but, I think it was worth the 15 dollars I payed for it; The set's big, and, it has pieces I know I'll use for both Johnny Thunder AND an original Sci-Fi brickfilm. - If I hadn't have gotten it, I would have been limiting myself, and thus, making some future projects of mine harder to fully realize with what was already available to me...
Another good example of a good opportunity brought about by another brand was this recent K'nex Yellow Submarine set I got. Not only am I a HUGE Beatles fan, but, I actually needed some of the pieces in the set, as, LEGO doesn't make anything similar/I couldn't find similar pieces on Bricklink. Thus, I took a chance, bought the set, and can say that I really enjoy it - Actually, I enjoy it so much, I actually like the K'nex figures more than LEGO minifigures!
To put things into perspective, would you ONLY eat at McDonalds for the rest of your life, or, do you think that you'll try some other fast food/home cooked meals ever again? ... Most people don't swear allegiance to one name-brand for their whole lives when it comes to food, clothes, or other appliances; so why do some brickfilmers refuse to animate with anything other than LEGO? - That's certainly a question in my mind that spawned just after reading Nathan's topic.
Onto the subject of altering/modifying LEGO:
Again, when I started out, I was much more of a purist. However, even back then, sometimes I'd opt for using a head that had teeth marks (courtesy of my little brother) for a villain minifig, rather than using a brand-new one. Sometimes, such things can really add to a picture, even if they are but small details.
I think that Doug Vandegrift did sort of the same thing for his "America: Outlawed" brickfilm; He choose not to dust-off his old western sets, as, the dust gave them more of a rustic and run-down look, something that an old western town would have had. When you watch his film, you don't really notice any of this, yet, just the fact that it's there did probably help inspire the filmmaker while making the film - and that's something truly special.
Just look at Vitruvius in "The LEGO Movie" - His staff is just a chewed up candy-stick. Not only does this give the character an abnormally large staff, something exclusive to only him, but it also just goes to show that the directors and animators really were thinking outside of the box when choosing props. I'd love to see more of that kind of innovation in brickfilms.
BTW, though I never plan on making a Lone Ranger brickfilm (at least, not at this present time) When I got some LEGO Lone Ranger sets, I realized that he looked so... old, compared to the Lone Ranger figure that comes with the Disney Infinity game set. The Infinity figure not only looks much more like the Lone Ranger, as seen in the recent film, but he also looks much younger, and not bald - just as the Lone Ranger should. So, I took one of these pieces, http://www.bricklink.com/catalogItem.asp?P=62810 (which I have WAY too many of, as it is) sanded the top of it, and basically made it fit on the Lone Ranger's hat like this: http://www.bricklink.com/catalogItem.asp?P=16175pb01 Not only does it satisfy me for a display figure, If I even did decide to make a Lone Ranger brickfilm, I'd probably opt for using my custom one over the official LEGO minifig.
Again, I think that it all boils down to style and preference. I've edited pieces and done such things as I've described because I think it not only benefits the brickfilm, but, also makes the LEGO more aesthetically pleasing to me.