Thought about your post and surprisingly my TZ doesn't make the cut. I've had it since 1998 and love it. I wouldn't sell it and am very happy with my collection. I definitely prefer more to less, but it's fun to think what 3 games would I drop down to.
Using your hypothetical, I'm only choosing 3 games so those 3 are going to be the most loaded. In reality, I'm not a buyer of LE versions, so this is purely hypothetical.
I'm big on theme integration, excellent art, fantastic music, and outstanding rules. I love TZ because it is high on all of these.
My three choices are all a blast to play and integrate the theme and theme assets perfectly.
1. EHOH 40th
2. JJP Pirates CE
3. Alien LV
The #3 spot is a tough call between Godzilla and Alien. I've played both and both are excellent. I give the edge to Alien. It's a wide body and has a different feel than Stern.
In the end, I would have three different games from 3 different manufacturers which would provide alot of variety.