I don't really wish for a conciliation between the styles of western and japanese RPGs because they are very much two separate genres, western always being computer incarnations of table top games, japanese releasaes always being about telling a story. They overlap in certain respects, but I don't think there's any formula of synthesis that could make a complete RPG experience. I think they should just do this:

Make good games. It's like the random battle argument. I don't have any problem with random battles as long as their paced well and the mechanics of the battle system are interesting. Also, the "Run" function in Final Fantasy allows the player to skip unnecessary battles or escape from ones. I personally use it to add some challenge to more recent FF's, allowing the enemies to be a few levels higher than my party than they should be. Can they become tedious? Absolutely. But all it takes is a developer to implement it well and it can make for a great game.

I think the one device I would really like to see gone is the super-secret-could-never-find-on-your-own sidequests. When you need to use a guide, I feel the game fails in a way. I mean like the Zodiac Spear, for a current example. Who the hell could have ever figured that one out if it wasn't in an official strategy guide or anything?