That wasn't the only time it happened in the SQ series though. SQ2 reset the accomplishments of SQ1. You could argue SQ5 is the one that reset SQ4's accomplishments as well. In which case SQ6 actually reset SQ5's accomplishments.
I think the point the Two Guys were trying to get across is that Roger was always destined to be a loser no matter how well he did. ("Life sucks, again.").
More characters is certainly a departure from previous SQs, though Sludge Vohaul pretty much came out of nowhere as the big bad of SQ2.
Well, that lack of a resolution is hardly the fault of SQ6. They probably expected to tie that up in SQ7. (The fan game Incinerations provides a decent resolution to the Stellar/Bea thing BTW).