In most of the games, the only way to get the best ending is to collect all members of the hero's army (108 fighters and support characters.) Some characters are only recruitable during or after certain plot events, and others can only be recruited when the hero performs certain tasks in a certain order. Some characters will outright reject the hero if you happen to say the wrong thing to them, (or, in at least one case, if you press the "advance text" button while they're talking to you.) If that wasn't bad enough, some characters can be killed during major battles, if you're not careful with them. You can't revive any characters who have fallen in major battles, so once they're gone, they're gone forever. As such, getting the best ending the first time out is all but impossible with these games unless you have a walkthrough handy.
There is an infamous case when General Teo's army attacks. One character, Pahn, stays behind to stall him in a duel. One could easily assume this is meant to be a Heroic Sacrifice for Pahn's earlier betrayal, because should he lose, General Teo will send him off to be executed and that's the last we ever see of him. In actuality, if he's been leveled and geared well enough, Pahn can easily win the duel and return to the hero's side. But you would have to actually be using him up until then and given he's a generic and not particularly useful character and there are literally dozens of better characters to make up your party of 6, he most likely will have sat on the sidelines up to this point. Oh, and he's one of the 108 stars and absolutely needed alive to get the best ending.
As noted below, Clive seems to have a knack for causing confusion and anger among players, due to how difficult it is to recruit him and/or finish his quest. Getting him in the first game required you to be completely lucky enough to see him in a town's inn. If he is not in the inn, recruiting him requires the player to exit the town, re-enter, and try the inn again. Several times. The odds of seeing him are very low. There was no detective-like character in this game to give you any hints on where to recruit him, so without a guide, there's a very good chance you can search the entire game screen-by-screen and never see him once.
Recruiting the "Flying Squirrels". The "easiest" to get is Mukumuku, who can either be found by examining the tree (three times, no less) behind the Genkakku home near the beginning of the game, or by taking part in random battles on the path from Greenhill to the Muse border. The rest have to be recruited by taking part in random battles on the paths throughout the Greenhill region, although the mechanics behind this set of recruits still aren't fully known to players (and their locations aren't apparent without a guide). You have to have a free space in your party, all of the recruits have to be obtained in a chain (Mukumuku must be in the party to obtain Makumaku and so on) and there is still no foolproof method to recruit them beyond extreme trial-and-error. The only solution people have come up with in recent years is to have Stallion in your party, run in and out of towns repeatedly to "reset" the squirrels' locations and pray that you find them. Thankfully, they're not required for the 108 Stars.
Clive's subquest is timed from the start of the game and runs on a very fast timer. The player is forced to go through a series of events within 21 hours to complete Clive's story - otherwise, it is impossible to finish the sidequest (barring the use of a Gameshark). If you want to see every part of his storyline, you will have to inevitably play the game as quickly as possible, because the time limit doesn't leave much room for error and there are several points when Elsa (the woman Clive is chasing) goes to places the player can't reach (or isn't told about) until later in the game.
Nanami's survival relies on several variables, which isn't helped by the lack of hints or information regarding it. The first part is ensuring that you've recruited all 108 Stars of Destiny prior to invading Rockaxe Castle (and have seen the scene where the hero receives the final spell for the Bright Shield Rune from Leknaat). From there, once you invade the castle and confront Jowy, you have to respond to the dialogue prompt which is displayed when Culgan and his troops appear ("Look out!" or "Nanami!"), despite the fact that it only flashes on-screen for a couple seconds and there is no warning that it will suddenly disappear. Doing so doesn't change the content of the scene (Nanami is still seriously wounded and brought back to Headquarters), but if you did it right, there is a one-sentence dialogue change to let you know it worked (a doctor asks to speak to one of the strategists in private). There is nothing else that clues you into this...
...and then there's the "good ending". It's fairly easy to find out that there is more than one ending (choosing to rule the kingdom gives you the default ending, which concludes with Jowy waiting on the cliff where you first began your adventure). Going back to Tenzen Pass and confronting him leads to both of you squaring off in a one-on-one battle. Here's the tricky part: if you kill him, you're automatically locked out of the good ending. You have to choose to defend every attack, even when he attacks you or goads you on. And even then, you have to go through two battles and continue to actively refuse his request to give his rune to you until the refusal option changes and Leknaat appears. Didn't save Nanami? You're locked out by default. Trying to work all that out without an FAQ is enough to break your mind.
To be fair, the game does foreshadow that you're not supposed to attack Jowy just like Genkaku never attacked Han in their duel and seal the Rune of Beginning together. Then again, it happens for so long that players may have forgotten about that part.