Thought of another one, involving Paladin's Quest (spoilers):
* In Paladin's Quest, there are two first-class party members. There's Chezni, who is the main character, uses fighter-type equipment, and starts with Fire magic. There's Midia, who is with you most of the game, is more mage-like in her equipment, and starts with Earth magic. It turns out, however, that Chezni gets Earth near the end of the game, but Midia never gets Fire, leading to an imbalance between the characters end-game, with Chezni being clearly the more powerful character, and it seems like the developers just neglected Midia in the end game.
* Also, at one point, you travel to the past. However, you can only explore a small portion of the world, and you can't return there after you return to the present.
* I could also mention that there's no mid-battle revive, and the final boss is so difficult that the game really did need one. (By contrast, Lennus 2 does have a mid battle revive, but it isn't as necessary there, with the final boss being *much* easier that time around.)
* (By first class party member, I mean that those two characters are the only ones who can equip new items or learn new spells after joining.)
I can also mention some issues with Dragon Quest 5 (again, there's a spoiler; also, this is based off the SFC version):
* DQ3 and DQ4 allowed you to make the main character either male or female; DQ5 doesn't give you the choice and instead forces a male main character (a problem that would persist in most later DQ games as well).
* For whatever reason, unlike every other Dragon Quest game from 3 onwards, you are only allowed 3 characters in the active party.
* Early on, there's a fight that you are supposed to lose; doing so will cost you half your money. At this point, you're likely to have an excess of money, and the bank isn't available at this point, so this feels rather cruel for the game to do this. (DQ4 has a fight like this, but it comes at the end of a chapter, and you don't keep money between chapters anyway.)
* You can recruit monsters, but the recruit rate is way too low for way too many of them; recruiting a Healslime is only a 1 in 32 chance, for example. (Recruiting a Healslime or a monster that's even harder to recruit is the only way to get access to Omniheal this time around.)
* Speaking of which, Multiheal and Omniheal are only usable during combat. Meanwhile, the Staff of Revival, which can revive a character for free with infinite uses, can be used outside of battle. (The fact that the staff can fail isn't a problem when you can just try again, and there's not even a turn cost for doing so because you aren't in a battle.)
* The weakest ice spell is, for whatever reason, not player usable, which seems rather odd.
* There's the Zoom spell (Return in older translations) that allows you to return to almost any town you've visited. For whatever reason, the use of this spell is blocked in many towns, even when there's no reason for it to be, and trying to cast it will waste your MP, which is quite annoying.
* Also worth noting that Chimera Wings, which act like Zoom in other DQ games, will only warp you to the last town you've visited in DQ5, which really does feel like a step back.
* Late game, you have two kids, a son and a daughter. The son gets to be the legendary hero, yet the daughter gets nothing. Furthermore, for whatever reason, the daughter doesn't learn enough spells to fill up her spell list window; she ends up one spell short.
Remakes of Dragon Quest 5 fixed some of those issues (the party size was increased to 4, Zoom now works unless doing so would break the plot scripting, the daughter's missing spell was filled with that one weak ice spell (which is useless at the point she joins, but at least it's now player usable)), but still left others in (low recruit chances for monsters, daughter still doesn't get anything special the way the son does).