At first, it may seem illogical with the Hive suddenly having a whole new sublevel that was not shown on Kaplan's 3D map from the first movie. But since only the top Umbrella executives planned to deliberately wait out the apocalypse in a secluded place to rebuilt the world from anew, they did not want an expendable assault team to uncover their secret plans and put them in jeopardy.
The real Dr Isaacs filling himself with cybernetic implants seems like a self-indulgent gesture, considering he spends as much time humiliating Alice as he does in actual combat. Then you recall how soon he was ready to do all that after just coming out of cryo-stasis. The cybernetic implants may have been necessary to survive it.
The implants would also have given him an edge in maintaining control after he and the other frozen super-rich awoke into an empty world. The other cryo-sleepers were presumably a bunch of power-grubbing sociopaths too, after all, if they'd been willing participants in real Isaacs's schemes in the first place: he'd have anticipated the need to foil a whole lot of coup attempts among the "cleansed" world's chosen survivors.
The Red Queen's actions in the last movie make more sense now that we realize she had recently learned the outbreak wasn't accidental. Her seemingly pointless interrogation of Alice was actually to verify she wasn't working for Wesker or Umbrella's leaders (given that Alice could be considered at least partly responsible for the outbreak), and her warning to Alice not to trust the "traitor" Wesker was also a surreptitious attempt to warn Alice of the trap Wesker probably had planned for her and the other survivors in DC.
Alice being a clone, might explain two reasons why, unlike basically everything else, she bonded to the T-Virus, making her superpowered instead of an mutant abomination, She is a clone of Alicia Marcus, her father developed the original version to heal her, so naturally Alice would be predisposed to the "benefits" of T-infection, not only that, but possibly the fact that Alice is an "edited" clone, the parts that caused the Progeria were taken out, either leaving "gaps" for the T-virus to fill in, or overcompensating for the lack of Progeria markers, making her superhuman.
Given that it is a relatively unique mutant, the creature Alice fights in the Hives dungeons could be what is left of Spence from the first film, seeing as the licker mutated Matt in a similar way, making Nemesis. It does look very similar to the super licker from the previous film, not only that, but its lair looks like a broken-down, dirty version of the train platform.
Alice blowing up a whole bunker of Umbrella employees who are frozen in stasis might seem to be overkill considering the state of the world, but it's not like letting them live would be better. For all we know, there are not enough resources left to supply several thousands people who might not adapt quickly to the new world. Not to mention that most of them would be Umbrella fanatics who, given the overall stupidity of the company employees, would end up destroying themselves in the long run.
