I can't remember which fossil I picked, and on which game. I must have gotten both in Emerald, and I'm quite sure I must have picked both of them in the R/S days since I completed my Pokedex and had to get Fossils for that. I might have traded over one of the Pokemon from a friend's game, but I doubt it.
As for which one I prefer, I don't really know. I never thought much about them when I played R/S, and I'm not sure now either. Armaldo is kinda cool but I have never used it much. It has a cool type combination, but it is rather slow. Cradily on the other hand is the only Pokemon I have a love-hate relation towards. Two times, in different Battle facilities in different generations, I have been up against Cradily in extreme stall battles. The first time was in the Battle Tower on Diamond, the second time in the Battle Maison on X. It happened during Double battles both times. This has made me very careful every time I face a Cradily in a Battle facility if I can't defeat it with ease. I also tried using a Cradily myself on my post-game team for Black 2 (currently in my signature!) but it didn't really change my opinion on it. Anyway, after writing all of that, I think I prefer Cradily over Armaldo, for the reasons described above. That said, I never used it in Gen 3 other than evolving my Lileep for Pokedex purposes.