Nothing surpasses chronotrigger even after all these years.
Two contemporaries of chronotrigger that were much different but still quite good are terranigma and seiken detensu 3.
Two games that claimed to be trying to do something similar mechanically that are RPGs are septerra core and anachronox. Both are for PC and should run on a potato these days.
The legacy of Kain series and in particular the soul reaver offshoot has a great story and time travel elements, but they're more action puzzle games.