Currently feels like the quest rewards are token compared to how much you get
for killing all the bots that are in the way... I'd start by quadrupling the
reward EXP for everything if it was all done by the same scale as the few early
quests that I've seen.

Perhaps. 
Perhaps they could be kept as tokens.
Perhaps they could be dropped entirely. In quests that are not necessary for progression, Tux can and in many already does, obtain other useful items - pills, gun, NPCs offering to teach him skills ...

obtains items:
data/storyline/act1/dialogs/Bender.lua:			Tux:add_xp(150)
data/storyline/act1/dialogs/Tania.lua:			Tux:add_xp(1500)
data/storyline/act1/dialogs/SADD.lua:			Tux:add_xp(1000)
data/storyline/act1/dialogs/SADD.lua:			Tux:add_xp(1500)
data/storyline/act1/dialogs/SACD.lua:			Tux:add_xp(1000)
data/storyline/act1/dialogs/Spencer.lua:			Tux:add_xp(100)
data/storyline/act1/dialogs/Duncan.lua:			Tux:add_xp(3000) (sell more items)

optional for progression:
data/storyline/act1/dialogs/Michelangelo.lua:			Tux:add_xp(350)

to keep:
data/storyline/act1/dialogs/Butch.lua:            Tux:add_xp(8000)
data/storyline/act1/dialogs/TutorialTom.lua:			Tux:add_xp(2000)
data/storyline/act1/dialogs/TutorialTom.lua:			Tux:add_xp(2000)
data/storyline/act1/dialogs/Town-NorthGateGuard.lua:				Tux:add_xp(70)
data/storyline/act1/dialogs/Town-NorthGateGuard.lua:				Tux:add_xp(100)
data/storyline/act1/dialogs/Ewalds_296.lua:			Tux:add_xp(1500)

?:
data/storyline/act1/dialogs/Kevin.lua:			Tux:add_xp(100)
data/storyline/act1/dialogs/c-net.lua:			-- Tux:add_xp(30) -- Eventually make this a quest goal.
data/storyline/act1/dialogs/Spencer.lua:			Tux:add_xp(250)