There are many difference but some one posted this great reference that I agree with and might add to in the future...
1) D20 has a unified die mechanic; with the exception of damage, d20
makes use of a d20 to resolve all conflicts/encounters in the game.
PFRPG uses a d20 to resolve combat, and d100 to resolve skill checks
(both use various other die types for damage).
2) D20 is an
interative level system, PFRPG a suceessive level system. D20 characters
can completely change archetype everytime they level, where as PFRPG
improve within their set archetype. This vastly changes the complexity
of "building characters"; after you build a PFRPG character at
1st-level, with the exception of improving some bonuses, they are a
fairly static character. Since D20 has interative levels, you don't stop
"building" your character, from 1st to 20th level (or beyond).
TL:DR version: PFRPG characters are more static, but less complex to build after 1st-level.
3) PFRPG let's you play as one of the "monster races", without having to buy a separate supplemental book.
PFRPG makes use of archetypical OCC's (or RCC's), rather than the more
general "Fighter" or "Cleric" builds. You can start as a Knight at
1st-level in PFRPG.
(this offsets the "well, I can play an Elven
Fighter/Mage in D&D, starting at second level...", with "Well, I can
play an Elf who can swing a sword and cast magic at 1st-level, in
5) D20 makes use of "Feats" to add customization of
characters in the game; while this adds diversity amongst the
characters, it also adds complexity to the game. And many combat options
freely available in PFRPG (disarm, trip, flip) are only optimally
usable in d20 with the investment of multiple feats (i.e. feat trees).
Defenses in PFRPG are active, rather than passive. This is a huge one,
and a major selling point for me. In PFRPG, I get Parries and Dodges to
avoid getting hit, rather than a static Armor Class. Personal skill (and
good die rolls!) mean more to my defense, than what armor I'm wearing
or what magic rings I have on. That's huge for me.
7) Armor in PFRPG is ablative, not deflective. Armor in PFRPG soaks damage. Armor in D20 keeps you from getting hit.
) Magic in PFRPG works off of PPE, which is like a mana pool, with
magic-users able to make use of any and all spells they know, so long as
they have sufficient PPE. Magic in D20 is Vancian "fire-and-forget".
Combat in D20 is automatically assumed to take place on a tactical
grid. PFRPG can be played on a grid, but it is not the automatic
10) PFRPG does not have the added complexity of Prestige Classes, when leveling your character.
11) Palladium books is a game that encourages role playing over hack and slash.
12) You can choose to choreograph every single combat motion in Palladium system, or role play you way out of challenging battles - D20 is a roll of dice succeed or fail then move on in the game - D20 is a faster paced focus on the game, while Palladium system is a character interaction focused game.
13) Palladium books has a number of fans who have strong opinions that do not always clearly point out source material for reference. D20 tend to have more friendly supportive fans of the game. So the message boards you hang out at might sway you in one direction or another. I don't mind challenging people so long as they know what they are talking about.
14) Palladium is a game that spans many genre's and characters can be easily integrated into all of them with minor changes. D20 games requires whole new books most of the time to enjoy a game in a different genre, often making you re-role a new character or switch game systems altogether to enjoy full. Palladium has managed to keep one system pretty well through all genre... It truly is a great system - You just need to understand the subtle differences in rules between books / genre your playing in with Palladium's system.
Like I said I may add more in the future to this.