The reason for the incest jokes
I think I understand why the writers have been using creepy, not to mention cheap incest jokes so often lately. Aside from the general drop in quality that is apparent, I think they've also put themselves into a corner with that premise. It's three whole families and nine characters (eleven with the babies) for a half-hour show. There's barely any time for supporting characters. Almost every episode includes the three families (or at least two of them) somehow intereacting within a storyline. I guess there's the Andy thing from time to time, but it's not in every episode. They obviously don't want to have someone cheat on their significant other, because it will seriously mess with the comedy element unless it's brilliantly written (the writers are hardly Larry David apprentices), which leaves very few possibilities for sex jokes unless they have some incest implications.
Now, I am not in any way defending this, it's creepy and unoriginal. But it also makes sense after 8 years. Two and a Half Men barely had one full family and it got beyond unfunny by its 8th season. The show should have ended much earlier to avoid all this awkwardness. It's too late now, so expect Manny to have mixed feelings for another relative very soon.