If you were to recreate Star Wars using only Joe characters, whom would you choose for what roles? Do you go by personality or appearance?

I say the bad guys are easier.

Cobra Commander as the Emperor. He's evil, wants to rule the world but will let you live in it as long as you follow his rules.
Destro as Darth Vader. He's big, he's bad ass, he wears a mask. He does have honor, but isn't above breaking your neck on a whim.
Firefly as Boba Fett. He's mysterious, wears a mask, no one really knows much about him but he gets the job done.
Storm Shadow as Anikan. He the best there is at what he does,but he's torn between the two sides.
Scrap Iron as Admiral Piet. That guy who does his job, does it well, and that can be relied upon
TomaxamoT as Jabba the Hutt. The leaders of a group of people who can infiltrate in to any part of society to get intel and info and manipulate the world to go the way they want it to go.
Crimson Guard as Jabba's minions. See above.
Blue Shirts as Storm Troopers. Gotta have the cannon fodder.
Zartan as Prince Xizor. Although not part of the SW movie canon, he'd be a good fit there.
Serpentor as Tarkin. A brilliant military leader, very disciplined and ruthless.
Baroness as Issard. Since the only woman in SW is Padme who died then became Leia,female characters are hard to come by so I reached outside the movie canon again. Cold hearted and mean, but she gets what she wants.

As for good guys, that's a bit harder
Shipwreck as either Lando or Han Solo. Cocky, independant, always working a deal.
Scarlett as Leia. She always came across as the strongest of the first three women, a good leader and fighter
Snake eyes as Obi-Wan. While SS is the best with the ninja skills, SE is more focused and disciplined and more of a mentor
Ace as Wedge. Hot shot pilot, a master behind the stick. Doesn't rely on ninja (Jedi) skills to get the job done
Bazooka as Chewbacca. At least cartoon Bazooka.A big galoot that you can help but love, he's always got your back

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I'd go with Serpentor as the Emperor, Storm Shadow as Vader, CC as Tarkin, BlueShirts as Death Star Officers, Vipers as StormTroopers, and Destro as Thrawn. FF as Fett is dead-on perfect, tho.

For the Joes, Chuckles and Mace as the Bothan Spies that stole the Death Star plans.

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I'm seeing a Group Project here.

Emperor: Serpentor
Moff Tarkin: Cobra Commander
Vader: Destro
Piett: Major Bludd
Veers: Voltar
Moff Jerjerrod: Tomax and Xamot
Admiral Motti: Dr. Venom

Fett: Firefly
IG-88: Overkill
Bossk: Big Boa
Dengar: Raptor
4-Lom: Wraith
Zuckuss: Crystal Ball

Jabba: Headman or Golobulus (not sure I want to go there)
Bib Fortuna: Gristle
Gammorean Guards: Headhunters or Royal Guards
Greedo: Black-Out (yes, he shoots first and misses... )

Garindan: Zartan
Ponda Baba: Torch
Dr. Evazan: Buzzer

Luke: Duke...because that rhymes...think of Renegades younger Duke, not the older Nam vet Duke.
C-3PO: Dialtone (the irritating tech guy)
RD-D2: Mainframe (the competent tech guy)
Obi-Wan Kenobi: Joe Colton
Han Solo: Shipwreck
Chewbacca: Gung-Ho (replace growls with Cajun gibberish)
Leia: Scarlett
Lando: Stalker or Alpine
Gen. Dodonna: General Flagg
Gen. Riekeen: General Hawk
Admiral Ackbar: Keel Haul
Gen. Madine: Colonel Courage
Mon Mothma: Jane
Wedge: Ace
Capt. Antilles: Capt. Grid-Iron...ha!...I was gonan say Cutter...but I'd rather Destro choke Grid Iron.
Nien-Nunb: Tunnel Rat
Biggs: Slipstream
Lobot: Psyche-Out

The Ewoks: Tucaros or whatever they were called.

I used to do this very thing as a child since I hated Star Wars figures. Mine was based more on appearance and several Joe's were used as new/original Star Wars characters, some of whoms names I do not even recall.

Han Solo - General Flagg
Destro - new Sith Lord
Baroness - new Sith Lord's apprentice
Mercer VII - Dash Rendar
Updraft - Wedge Antilles

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Sean_c, I like your idea of Renegades Duke as Luke. He was a hard one for me. Someone young and still needing to learn about things, but still has a little bit of worldly experience. Renegades Duke in ANH and Resolute Duke by ROTJ.

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Hmm i'd say roadblock as chewbacca