I'm surprised to find that I've only played 2 JRPGs, Breath of Fire and Dragon Quest 8, both are favourites of mine, Breath of Fire in particular. I agree that JRPGs are linear and the story is often the same, gathering companions, travelling the world, sticking it to an ancient evil. But then this is exactly the same as Dragon Age Origins and the Mass Effect series.
My thoughts on BOF, DQ8, DA:O and ME1/2:
The difference is the approach they take to this "save the world" mold and I take different pleasure from both.
For BOF and DQ8 its the journey, the slow gathering of companions and skills as you traverse the land and finally return home.
For DA:O and ME1/2 its the character interaction, I play these games solely to get new conversations.
But for me BOF and DQ8 win other DA:O and ME1/2 because of epicness. All four games are epic in there own way but the epicness of DA:O and ME1/2 often appears in cutscenes, Shepard becoming a spectre, his first speech as captain of the Normandy, Sarens appearance on Virmire, same can be said for ME2. Rarely does the epicness crossover into the gameplay.
Side note - ME2 is definitely more polished and with great features (love those interrupts) but ME1 is imo the better game the epicness those cross over into the game more often, diffusing the bombs on Eden Prime, Virmire, Illos even the final boss is more threatening. In DA:O the only time it truly felt epic was when I said my goodbyes to my companions and ran down the street into the heart of the city with npc's cheering, the reputation of the Grey Wardens finaaly restored.
In DQ8 the epicness always comes up during the major boss fights when you're in control.
In BOF there's just no contest in epicness the moment the final overworld theme beings to play.
In summary these two JRPGs are most epic when you are playing while the other two are most epic when you are watching.
My thoughts on Fallout 3 and Oblivion:
Are they really RPG's? I've played both and I enjoy both but arent they just sandbox shooters/slashers where the role playing element is just you deciding which is your main weapon and armour of choice. You have very little effect on the missions and your approach will often be in a linear fasion, how often in a given mission can you go through a different door, sneak in from the back etc. Fallout 3 is a definite improvement but still if thats an RPG isnt Far Cry 2 also one and a better one at that. You have to aquire your own transport, aquire funds, aquire specialised weapons, your only told where to go everything else is down to you.
Finally my two favourtie WRPG's would be Deus Ex and Vampire Masquerade-Bloodlines. Deus Ex wins with level design while VMB has a deeper level of interaction with the npcs.
OT: I'd say WRPGs as some of them really let you role play.