as of now, i think a good list of checkpoints would be
>julia
>florinia
>corey
>shade
>aya
>noel
>luna
>charlotte
>ciel
>adrienn
>amaria
>hardy
>elite 4
>t2.5 postgame
>t4 postgame (jirachi)
>t6.5 postgame
>final boss

HOW TO GET GOOD ENDING:

reborn has a multiple endings system, which will drastically change several things about the postgame. in order to get the...ending where less unfortunate things happen, you must do the following things:
>Rescue all the police officers before the Ace fight in Rhodochrine
>Beat the Garchomp on Pyrous
>Don't fight Sigmund in Yureyu
>Stop Sigmund at Tanzan
>Side with Radomus at the Citae
>Don't give Blake the ruby ring
>Don't fight Taka at the WTC
>Take Taka with you in the desert
>Defeat the champion without whiting out

nothing super major will REALLY change if you decide to get the...less fortunate ending, except you might need to be admitted to a mental hospital afterwards