They didn't change it so much as just have the character (whichever one went inside) wake up a week or so later and continue the story. You still get the Ron Perlman voice over.
As for the comparisons to Mass Effect, granted I've only had it a few weeks (since Steam was giving it away for a fiver) but I think both games are quite evenly matched, with perhaps a few points away from MA for general, mild blandness and copy-paste environments (I'll never complain about FO3's metro tunnels again!) Both have less than perfect combat mechanics, NPC AI, a number of odd engine bugs and feature an engrossing world and story that on closer inspection turns out to be quite thin on revisitability (new word?)
Put a gun to my head though and I'd have to go with FO3 by a nose, if nothing else than for the sheer immersion factor...even if walking around the Citadel made me pine a little for a similarly conceived Babylon 5 game.