Deadly Assassin was another biggie. Hell, they were pretty severe in their first appearance in The War Games, and the Time War wasn't the first time they tried to erase the Daleks from history. (I don't know from the radio series and am not even going to try to get into what happened there and what is and isn't canon, but I watched the Eighth Doctor remake of Shada and Romana was President at that point.)
I think a post-Time War Gallifrey would be a whole lot different from the one we saw on the old series. We've already had hints of how much the Time Lords (and the Doctor in particular) changed -- enlisting in the Master's aid is a nontrivial change.
And who's to say what role Dalton's playing? He could simply be impersonating a Time Lord. Or it could be that there's a NEW race attempting to assume the Time Lord mantle. Hell, it could be some Wibbly-Wobbly Timey-Wimey business where they're meeting with a Time Lord who eventually dies in the Time War but hasn't yet when they encounter him.
But given that it's RTD we're talking about? I'm going with "something over-the-top and ill-conceived that serves to completely undermine something much better that he did earlier in the series." (Of course, it hardly even bears mentioning that the Time Lords' sacrifice has been pretty fucking-well trivialized by the fact that the Daleks keep showing back up every year on increasingly ludicrous pretenses -- the latest being "I am the last of my race and want to destroy my race, so I'm going to go back in time and save my creator so he can make a bunch more of us". Bringing back the Time Lords and the Daleks in earnest would get rid of that dilemma -- and I'm not opposed to Dalek stories -- which is good, because they're pretty much inevitable --, I'm just opposed to seeing one every fucking year; I'd love for them to go back to the "one Dalek story per regeneration" rubric. #4 had one good Dalek story and one mediocre one, #5 and #6 had a good one each, #10 had one good one and two bad ones. #9 managed to buck the trend by actually having two pretty good ones, and I haven't seen Remembrance yet so I can't vouch for #7 but I hear it's good.)
...But I think of all the theories I've just pulled out of my ass, I like "new race attempts to assume the mantle of the Time Lords" the best.