Just by looking at the guild fort scores, you notice a trend: CoM, VG, CJ, CXE, NAL, Cruxis, SOS, ZC, Pulse, BoN, AV, and many, many more, ALL use the sub guilds as allies system. If some of you believe that this is abusing the allies, then that would be more of a reflection on the tower system itself, not the guilds. For those who say it's totally possible to be successful with one 25 member guild, check the top 50 and see how many of those actually exist.
As for loyalty, most tower guilds prioritize loyalty from their members. Of course some guilds noobcruit and win that way, but most of them do have a solid set of perms. I think most PC players are used to smaller, more tightly knit guilds simply because the PC community is smaller & generally has less kids. For example, on a server that averages 100 players, having a loyal guild of 5-10 is pretty impressive. On a server with 1500+, you really do need some way to give your guild a chance to win (Subs as allies). I see no problem with both guild types (Small, no sub allies, and large, subs as allies) coexisting, no need to fight over it.