all games are not created equal

It's nice to see Harmonix dip back in it's roots a bit :)

Rock Band Unplugged basically borrows the entire gameplay from Amplitude and adds a layer of Rock Band paint.  You control every instrument and jump from track to track.  When you play a couple bars of the instrument flawlessly, it "unlocks" for a few phrases while you immediately jump to the next instrument.  However, key differences leave Amplitude a step above RBU.

The difficulty in Amplitude is far better than RBU.  Both games offer easier levels, but even in Expert mode, RBU still feels pretty easily, espeically to vets of rhythm games.

The soundtrack probably goes to RBU in this comparison, for one simple reason; expandability.  RBU, like it's bigger console brothers, allows you to purchase songs for download onto your memory stick, allowing you to continuously purchase and play music as time moves on.  Amplitude existed in a time when no such feature existed.  Also, RBU features more songs on disc than Amplitude does, though Amplitude features some trance/dance/techno songs that appeal to me, so I still prefer Amplitude's soundtrack.

The gameplay is mostly the same.  However, RBU does a smart choice by forcing you to play an entire solo (for whichever instrument) instead of just playing a couple bars as normal.  Also, you can choose to play just one track the entire song if you so choose.
However, Amplitude allows you to freestyle when you collect a certain power-up.  The freestyler will either let you control a synthesizer or a scratch table for a certain length of time, which allows you to add your own little flavor on a song.

However, Amplitude completely excels in two areas.
Multiplayer doesn't exist in RBU.  There's not much more to say than that, other than it's weird that a game as focused on multiplayer as Rock Band doesn't feature a multiplayer option in it's portable iteration. 
Amplitude, however, features a plethora of multiplayer options, though all are competetive, save for the Remix function.

Oh yeah, and last thing.  Amplitude lets you remix songs in the game!  You can take any song that you've unlocked, and go into a remix mode that allows you to put down your own drum beats, guitar rhythms, synth noises, etc etc.  Back when Amplitude was new and had a crowd, going online and downloading remixes was possibly the best part of the game.  To this day you can still youtube remix videos from this game (and Frequency alike).

RBU is a good distraction for a music lover on the go, but Amplitude just offered so much.