(Assumes you pick the girl as Torchic and boy as Mudkip)
						Torchic			Mudkip
Rival text				-7
Wild Zigzagoon		
Rival 1					
Calvin					-1
Seedot hunt				-1
Surf friend								-30
Zig catch				-29	
HM overwrites							-14			
Aqua Pooch				-2
Rock Tomb teach			-13
Museum Zubat							-4
RT for Plusle/Minun 					-1
Sell RT					-6
Rival 2 save			-9
Rival 2 deaths			-11
Rival 2 fight 							-2
Rival 2 items			-6
Rival 2 experience		-21
Rival 3	fight							-8
Rival 3 experience						
T&L										-1
Dive friend								-44
One fewer VR Revive		-5
E4 PC deposit/HoF								
TOTAL					-111			-104

(Assumes manipless; Torchic is likely faster in a manip run because you can manip Marill, but it depends on the experience route and the player's ability to hit manips often enough to justify skipping the Rival 2 save)

(Timings for girl Mudkip)
						Torchic			Mudkip
Wild Zigzagoon		
Rival 1					
Calvin					-1
Seedot hunt				-1
Surf friend								-30
Aqua Pooch				-2
Rock Tomb teach			-13
Museum Zubat							-4
RT for Plusle/Minun 					-1
Sell RT					-6
Rival 2 save			-9
Rival 2 deaths			-11
Rival 2 fight 							-2
Rival 2 items			-6
Rival 2 experience		-21
Revive for Flannery		-9
Rival 3	fight			-13
Rival 3 experience						-2
Cut candy benefits		-8
T&L										-4
Dive friend								-44
One fewer VR Revive		-5
E4 PC deposit/HoF						-2			
TOTAL					-105			-89