Apologies for the fairly scattershot approach to this but I'm just typing as thoughts come to me...
Have a read of the rules for the Star Wars LCG then pop back here...
Objectives - A fantastic way to tell the L5R story, the cards that come with the objective sets can also relate to the story. They also present a way to get around strongholds and allow you to feature multiple clans in your deck (still a balancing act to make it effective). Objectives generate gold to purchase units.
You attack Objectives which can also be story driven tying the warfare together with the characters. Objectives also interfere with he game in various ways.
Objectives also drive deck building in a very story driven way.
Comitting characters to the Force - Honour Victories - send honorable character to the imperial court to tell your tale. Whoever has the most honour at this point can advance their honour dial OR they can add damage to an objective. This kind of blends the Imperial Favour in with the win conditions.
Military Victories become destroying 3 Objectives.
Battles can be very similar - Edge battle allows for maneuvering/tactics tricks etc and then striking allows plenty of ways to make warrior type characters different from courtiers and Shugenja.
The more I think about the more I think a slightly fiddled with re-skinned SW LCG would be quite fun as an L5R LCG.
Another bonus - the games are shorter.
Edited by DWRR