The question I have regards two of the rules on the FAQs and erata sheet.

firstly, that super crises are immune to all character abilities affecting crisis cards and skill checks.

Secondly, that Apollo may use "alert viper pilot" ability whenever a viper is placed from the reserves.

the first seems to not want any super crisis to be effected by character abilities but the second has no restraints.

In the core game (which is the only one I've played so far) when the "Massive Assault" supercrisis is played it is therefore possible for Apollo to pilot one of the vipers that are deployed and then take an action. In that action he could xo the admiral and nuke everything, or use his OPG and launch 6 more vipers making it more like "massive ambush" for the cylons, or he could xo someone to use their OPG, in the Pegasus game that could be admiral Cain. She could Jump out of there making the special rule for the crisis (back two steps on the jump track) mean nothing whilst clearing out the enemy fighters and the revealed cylon who played the card hasn't even finished their turn.

My question is, have the designers realised that, though no other character ability is allowed to, "alert viper pilot" has the ability to seriously undermine a supercrisis card? and what would you do if this situation came up in a game?

i apologise if this has already come up but I couldn't find it discussed anywhere.

The faq states (in the errata section):

"On page 19, the last sentence about super Crises should read: "Super Crisis Cards are treated like normal Crisis Cards, but are immune to all character abilities that affect Crisis Cards or skill checks."

(Not bolded for emphasis, it's a straight copy/paste.) So, I'd green light Lee's alert viper pilot ability.

His ability doesn't actually affect the Crisis card and Massive Assault has no skill check. That rule is simply to prevent people from janking Super Crises with Starbuck or Sharon or tweaking the skillcheck in their favor with Adama or the Chief.

Apollo's fine to launch and shoot something if he's Lured into a Trap or Massively Assaulted.