I would be all over some of these sets if they were to be made, but some of the figure choices seem rather odd, no offence. Here's my take on your suggestions:
Jedi Temple Assault:
-ROTS SA Clone Trooper with blue 501st paint deco
-2 Blue Lightsabers
-2 Green Lightsaber
-2 DC-15 Rifles
-2 DC-15 Heavy Rifle
-2 501st Clone Trooper Helmet
-2 Jedi Cloaks
-1 Jedi Padawan (Zett Jukassa body with new head)
Star Destroyer:
-OTC TIE Fighter Crewman with new arms (similar to those of the At-AT driver)
-2 E-11s
-2 OLT-19 Heavy Rifle
-1 Mouse Droid
-1 Star Destroyer Command Console
-1 Red Lightsaber
-1 TIE Fighter Storage Crate
-1 Storm Trooper Helmet
-1 Imperial Comlink
-1 Macrobinoculars
Utapau Invasion:
-TSC Clone Commander (Repainted Orange) [I assume that this is the Windu Squadron Clone Commander?]
-2 DC-15 Rifles
-2 DC-15 Heavy Rifle
-1 Jedi Cloak
-1 Battle Droid Blaster
-1 Blue Lightsaber
-1 Green Lightsaber
-1 Republic Gunship Storage Crate
-1 Republic Gunship "Bubble" Turret
-1 Magna Guad Electro Staff
Hunt For Sun Fac:
-Boss (Scorch repaint, with new game-accurate accessories)
-2 DC-17 Rifles
-1 DC-17 Sniper Rifle
-1 DC-17 Grenade Launcher
-1 Geonosian Sonic Blaster
-1 Geonosian Electropole
-1 Battle Droid Blaster
-1 Tow Cable
-1 Treadwell Droid (Repainted Black) <--possibly replace the droid and the
-2 Hangar Bay Crates crates with a geonosian or battle droid?
Heir To The Empire:
-Grand Admiral Thrawn (Repainted White Veers Body w/ New Head)
-2 E-11s
-2 OLT-19 Heavy Rifle
-1 Mouse Droid (Repainted Light Gray)
-2 Ysalamiri
-1 Black Jedi Cloak
-1 Brownish Orange Jedi Vest
-1 Green Lightsaber
-1 Blue Lightsaber
-1 Blaster Pistol
Cantina Skirmish:
-Kit Bashed Cantina Alien
-4 Barglasses (Assorted)
-1 Bar Table (Like The One Packed In With TSC Hem Dazon)
-1 Blaster Rifle
-2 Blaster Pistols (Assorted)
-1 Imperial E-11 Rifle
-1 Lightsaber
-1 Sandtrooper Pike
Hoth Attack:
-TSC Snowtrooper with new, poseable arms and legs
-2 Imperial E-11 Rifles
-2 Rebel Heavy Rifle
-2 Rebel DH-17 Pistol
-1 E-Web Repeating Turret
-1 Crate
-1 Snowtrooper Backpack
Assault On Naboo:
-E1 00M-9
-2 Battle Droid Rifles
-1 Naboo Grapple Gun
-2 Naboo Heavy Rifle
-1 Jedi Cloak
-2 Naboo Security Blasters
-1 Green Lightsaber
-1 Blue Lightsaber
-1 Comlink
-2 Gungan Energy Balls
-1 Nute Gunray's Mechno-Chair
-1 Sidious Hologram
There's my take on it, but overall, you came up with some fantastic ideas for these, HunterofThePegs. I wouldn't mind seeing either of our takes on these on the shelves one day.