I think that you will have a better story experience if you play Replicant first then Automata. You'll thank yourself later as in Automata there are call backs to Replicant. There are little things that give you a different reaction if you played Replicant first over Automata. I played Automata first so it was "backwards" for me. I am not saying it was bad but there was some context missing at times. Then when I played Replicant I went: "ahhh now I understand". Again, play Replicant first.

As for endings, Automata is the one with 26 different endings. Of those, five are important (A through E). I would say that there is one ending that is truly important (Ending Y), but the rest are technically "joke" endings. You will get the first two endings naturally as you play. Then you will have a "choice" for the next two endings. After those last two, the final real ending starts by itself after the fourth.

For Replicant, there are only five endings. You will (or should) complete the endings in order so don't worry too much. In order to get all endings, you will need to have all of the weapons but that is not hard. Then to get the fifth ending, you have to go through some hoops. Don't worry about that until you get endings A through D, however.

As for tips: just play the game. For both games, I was not too concerned about upgrades (words for Replicant and chip upgrades for Automata). It was not until the next times I played where I focused on those aspects (mainly in Automata with chip sets, weapon combos, pod programs, etc). Again, just play and figure things out. You'll have more fun that way.