For a number of characters who still need upgrades (Alice really needs something flashier now- she's begging for a funnel style onslaught with dolls), last words do make good options for new finishers. So it's quite possible a few could get used.
Regarding survival cards, that's not really relevant to this gameplay- Flandre had survival pattern, and it was kinda dumb in execution and a little unfair to the player. They might still be a rare gimmick in the future, but I suspect even if the pattern was a survival card in the source game, they'll just have it play by normal boss rules in this game. That is to say, a barrage pattern with a lagre and awkward to navigate shape, unavoidable special effect, massive debuffs to you, a full HP and EN recharge with new weapons, stats and/or abilities, and you only having a couple of turns to beat it before it expires and you miss out on exp, money, and drops.
Eiki will very likely show up since Komachi's already around, it might be in 4 but it could be in 3 if they don't make a huge thing out of PoFV's events and give it only a couple of chapters or if UFO, SA, or IN don't take too long or don't actually resolve in 3. The timing of these events are all off and resequenced anyway, so presuming it happens later just because IN will be handled in 3 is somewhat faulty. After all, Mountain of Faith events starting kicking in before Embodiment of Scarlet Devil got really moving and was finished before Perfect Cherry Blossom even started. Though I do think it will be an early part 4 event just because they've already foreshadowed 3-4 (UFO brings Mystic Square along with it) other games; unless SA doesn't actually get dealt with in 3 and it's been reserved as the ultimate threat of the collective game. Utsuho does present potential worldwide destruction and has the malicious intent to do so after all...granted not the intelligence to pull it off, but it's the thought that counts. So I think it's also very possible they are really only teasing SA and the subterraneans won't actually become a major issue in 3.