I've been thinking about the game a lot since having my first child last year. She often lifts things and rotates them in her hand just to see and experience them. When I was a kid playing Shenmue I always found it funny that they added that mechanic because "who does that?" but now I feel a very deep appreciation for it.
At the time it was a unique, first of it's kind, game. Now there have been a lot of advancements since then so I didn't have the same "Wow" feelings of just being in the world. But the nostalgia still hit me hard and it still has a special place in my heart.
It's similar phenomenon to people hearing the Beatles or the Rolling Stones (or any of the artists they ripped off ...) with modern ears.
There's hope, though. I do think in both cases, it's possible to develop an appreciation once you learn about the lineage of a particular work.
I guess it depends on what you're trying to accomplish with playing Shenmue now. Is it the story or the immersion?