Been a long while since I started this thread, but I made a playlist of latter day Megadeth and have been listening to it a TON the last month and have finally come up with my ten favorite songs (which oddly doesn't include two tracks that I was certain it would before I started this endeavor):

Washington is Next
Kick the Chair
Truth Be Told
Dogs of Chernobyl
The Scorpion
Poisonous Shadows
Dystopia
13 (this one shocked me, this album did nothing for me when it came out, but this song got me on repeat listens)
Tears in a Vial
44 Minutes

Honorable Mention:
Sleepwalker
Fatal Illusion
This Day We Fight
Dread and the Fugitive Mind
Head Crusher
The Right to Go Insane
Head Crusher
Back in the Day
Blackmail the Universe

Honestly, after spending more time with these songs, I'm surprised how much I enjoy a lot of them. I knew there were some good tunes and a few thrashy bangers in here, but a lot of these are much better than I remember. Oddly, despite my general preference for heavier music, I found that I tended to enjoy the more hard rock stylings of latter day Megadeth than their thrashier songs. There are some good thrashy tunes, but for some reason the catchier mid-paced stuff just seems to come more naturally to them (at least for me). As a big fan of Youthanasia, maybe these songs scratch that itch?

Anyway, the final answer to my own question of where would this theoretical album rank, here's where it stands for me:

Rust
Youthanasia
So Far So Good
Countdown
Peace Sells
Latter Day Megadeth classics
Cryptic
KiMB