As we all know, there's a rampant problem with the amount of exiles/teleportation being abused.
1)Villages have been abusing the exile/ pardon feature to get quick movement to rogue villages(Ie, host lab, takumi, tanzaku) or vice versa(getting into leaf/sand/mist) without having to travel. This may not pose as an imminent problem, however it does make things such as the house teleportation very abusable. Not only this, but if you are to be exiled in an RP sense, it does not allow for a return to the village whenever you deem fit.
My idea to prevent this from being abused? Implement the same feature now used in corps. If you are exiled, you must wait 30 days(rather than the corps 180) before you can return to the village. This will put more of a sense of urgency behind the exile and pardon features to prevent them from being abused, and force village leaders to make these calls strategically.
2)The next rather important issue is the issue of teleportation/ quick map travel. more than once I've watched ninja run into a house and log off. only to appear in their home village free of BI, carrying whatever mission(Generally Docs) they've completed safely without worry of dying on the way. I feel as though I don't need to go into great detail on this one, as we all know this is not how @Ueda intended it.
Along with the house teleportation abuse, there is the issue of the "Hidden Kage Room". A room kages can carry their entire party into. Long ago, I never thought this could/would be abused. But now you will find when a group of ninja is pinned in a situation they cannot hope to escape from; the kage can team up with them, and teleport them all to that room. Safely in the village. This can also be done with bosses(Ie, Spider Boss/Snake Boss). Anything really that will teleport your team.
This can be a bit trickier to fix. As far as the houses go, it may be as simple as making it so you go through the same actions as death(Potentially minus the BI) to ensure it is not abused for mission purposes. Elsewise you can lock houses to villages so that (for instance) a leaf ninja cannot enter a sand ninjas household, or vice versa.
The kage room can be fixed by making it a door in the kage office similar to the chunin entrance building. Where kage can lock/unlock the area as they please to bring people in and out. This would remove the need for teleportation altogether.
Lastly for the bosses, you could make it so that each member has to elect to enter the room. Now that instanced maps are a thing, I imagine it would be easy enough to make sure you enter the same room as the rest of your party.
These are just some ideas to fix some fairly broken mechanics in the game. Input is appreciated, but if you're only shooting them down because you enjoy to abuse them yourself then keep scrollin'!