Tough call
Cole's definitely got the AP and durability advantage. Cole performed a 21 kiloton feat early in the game, and Evil Cole is canonically 2x stronger than is Good counterpart, so that makes it 42 kilotons to Alex's 228 tons - 1.97 kilotons.
Cole is resistant to absorption at the atomic level, so Alex ain't gonna be eating him anytime soon.
Conduits have a really strong resistance to diseases, plagues and toxins, so he may be able to fight off Blacklight/Redlight.
However, Alex more likely than not can grow resistant to Cole's lightning (Rice explains why in Prototype blog), so that's something to take into consideration. However, Alex needs to be exposed a few times to gain a resistance, and Cole is coming in with a massive power advantage, and Prototype has a bad history with electricity (Alex getting tazed by Cross, a Hunter getting blown up by touching a the third rail of a subway track, and Hydra's being subdued by a taser [until Heller came in and caused it to freak out]).
Alex's regen is an issue here, but it's dependent on the amount of biomass he has, so the more injuries he takes, the more biomass he loses, and the worse his healing factor gets (he couldn't regen his limbs after getting mulched by Heller in P2).
So, with Cole's higher AP and utilizing Alex'a weakness, and the fact that Evil Cole is ruthless, Cole should be able to vaporize Alex, given that Lightning Storm is stronger than his normal attacks, and can amp himself with Karmic Overload.
