I have been mostly labbing Cloud so I don't have a lot of new info but.
Down-Throw when opponent is out of stage does not true combo as someone had mentioned. It does put your opponent at the perfect position to D-Tilt him but your opponent can act faster than you can. So no combos there,

. (Tested vs Sheik)
N-Air now true combos into D-Tilt, Jab, U-Tilt and Grab as far as I know. I also tried doing Disable and F-Tilt, opponent was able to shield.
Still need to test with aerials, but I doubt any of them true combo.
Interestingly enough we got quite a few new kill confirms now since we can N-Air into Jab into U-Tilt into U-Smash or N-Air into grab into Throw, etc. There's also N-Air into U-Smash which is a true combo but requires you to be about at least Full Jump's height in order to perform.
N-Air is now a combo starter AND a kill move, 2 things it wasn't before. It can also still extend combos like it did before and do it in a safer way since there is less landing lag.
N-Airing through your opponent should now be completely safe on block. Before patch only chars with outstanding run speed (Falcon, Fox, Sheik) could punish this technique. With the reduced landing lag now Mewtwo can probably shield/spot dodge any punish thus making it safe on block (but putting you in a bad position).