Many people on this server who have spent time farming shards to go into the other factions city find it difficult to travel back, or to other places due to the portal not allowing cross faction travelling. So, why not allow Horde characters who have at least neutral reputation to use Alliance portals, vice versa? For example, take a Human who wants to go Silvermoon. He/she has neutral reputation with it, and use the portal at Shattrath instead of walking all the way. But the human can't use the other portals to Orgrimmar, Thunderbluff etc etc.
I'm not sure we're capable of changing the portals in that way, but I'd need Kretol to verify that.
There is, at least, working portals to Orgrimmar and Stormwind, which are the primary "hubs" for the two factions, in Shatterspear. Going from Orgrimmar to Undercity/Silvermoon isn't particularly difficult, nor is going from Stormwind to Ironforge.
I'm not particularly sure if making it easier for people to enter opposite-faction capitals is really something we want to do, anyway.
Grak is correct - there's no way to set 'limited access' on a portal to those that have enough faction with a particular city. It's either Horde-only, Alliance-only or Both.
Oh well. It would be more convenient, though.
If it can only be Alliance-only, Horde-only or both that's really no help to anyone, someone might go through the portal by mistake and get Roflpwned by the guards. I almost done this one or twice since I'm used to playing Alliance :P