How about:

- Your secondary can only be the same level of your primary or under.
- Your secondary is restricted from joining the following guilds: merchant,
alchemist, putyourguildhere.
- Your logins happen through your primary character's login, you choose which
one you want to play this boot.
- The finger message, as Zin said, would show who is whose secondary.
- Eq sharing should be allowed (perhaps because it's such a bother
implementing 'owner only wear'?), but I think tp-sharing would be just too
unfair toward those who have no boons/tp's.
- Maybe some restrictions on exp pool (maybe no exp pool for secondary at
all?)

Those are some thoughts on the subject. I'm neither pro nor con in this issue.
And reading all your posts i'm not quite sure if it would actually harm
gameplay or not. It's surely a nice new thing to try out in any case.