Here's my list of annoyances:
1) 1-byte/2-byte arbitrary limits.
For example: Might and Magic 1 and 2 where the maximum level was 255. I know back then there were data storage limits and disk space was measured in megabytes, but there's no place for those limits in modern games.
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2) Consumables in combat.
A lot of classic role-playing games had scrolls/potions/wands that hold a specific ability/effect and can be used a limited number of times. The problem: This forces the game to be balanced around using consumables instead of actual skill. If you are good at the game but were understocked on consumables, you could lose. Conversely, if you were bad at the game, you could just grab backpacks full of scrolls, potions, and wands - and win anyway. Earlier Might and Magic games (and other knockoffs of the series) had special resources (such as gems) that you needed to use most of your abilities. If you ran out of them, you couldn't use many of your abilities.
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3) Final Fantasy knockoffs.
(*puts on flame repellent*)
All sound and graphics with nothing between the ears combat-wise. Lack of tactical depth; no tactical movement. Romance in the storylines is a further irritation (IMO romance has no place in any video game). I'm probably going to receive heavy criticism for this, but IMO Final Fantasy is the mother of all bad role-playing games.
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4) D&D (Dungeons and Dragons) mechanics emulation.
D&D is way too clunky, burdensome, and bogged down by realism to make a seriously good game. IMO: D&D is to role-playing games what the Wright Brothers' original flying machine was to aviation. A good original first start, but you want to ditch it for something better once you have the technology to do so. I much prefer having player skill and character gear/build determine most outcomes instead of rolling dice for everything. Dice rolling and RNG does have its place, but it's just irritating to have 95% of stuff rely on a d20 roll.
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4b) No dynamic energy regeneration.
Most classic role-playing games emulated D&D's "abilities recharge only when you rest" balancing. This meant that if you wanted to recharge in combat, your only option was consumables. Newer games usually feature a talent grid and mechanics where you are rewarded with energy regeneration for using abilities properly.
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4c) Nonsensical combat ability restrictions that are in place only to fit with lore; designing around lore instead of proper combat balancing.
One example: Might and Magic VI. Sunray does lower damage than Dragon Breath with no area effect - at the same cost. Yet Sunray only works outdoors in the daytime while Dragon Breath has no such restrictions. Divine Intervention only works at dawn or at dusk, ages your character 10 years, and costs 5x as much as Lloyd's Beacon (which will get you to a temple where you can heal up for virtual pocket change and doesn't age your character)
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4d) Random chance to miss.
Good thing that Bethesda ditched those in later Elder Scrolls games (Oblivion and Skyrim). Most modern role-playing games and MMOs have also removed random chance to miss or at least have options to remove it.
In Guild Wars, for instance, characters didn't normally miss or get blocked/dodged - if you were missing, it's probably because blindness (condition) and/or certain hexes could cause characters to randomly miss. There was no constant block/dodge chance either - those were done with stances and buffs.
World of Warcraft has random chance to miss/block/dodge, but you can fix that with gear, talents, and positioning.
Most modern action role-playing games use an FPS engine where you hit or miss based on how good your aim is.
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4e) Conditions and debuffs on characters last until removed and can even get worse over time
In most classic role-playing games, harmful conditions (poison, disease, weakness, paralysis) need to be removed with an ability or at a healing facility. In some of them (see also: Might and Magic 3-5), they get worse over time. I much prefer the standard MMORPG dynamic where conditions and debuffs have a certain duration and then expire.
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5) Poor warrior vs. caster scaling/balance, late-game warrior inviability in classic role-playing games.
Most classic role-playing games feature nothing special that non-casters can do - they can just melee attack or range attack with nothing special. If it's a D&D clone, there might be feats to multi-strike, area strike, taunt foes, or change your damage/accuracy bonuses - and that's about it. Meanwhile casters have dozens of abilities to choose from. Another big problem with classic role-playing games was that casters usually scaled much better than warriors - so your fundamental adventuring team build decision was how to get enough warriors to "carry" your casters to upper levels, and then your warriors would drop off until they become irrelevant.
IMO a better way to handle warrior/caster balancing would be:
Warriors:
-single-target/small-area damage
-"normal attack" DPS
-sustained DPS
-Ability use mostly limited by cooldown, positioning, and combos
-Taunt and distract foes
-Buff team with commands and gear modification
Casters:
-large-area damage and DoT AoE
-ability use as big part of DPS; lousy "normal attack" DPS
-burst DPS
-Ability use mostly limited by energy reserves and recharge mechanics
-Stun and disable foes
-Buff team with healing, summoning, and other support abilities
Armor:
-Should be limited per class rather than class archetype.
-Main tradeoff: more armor = lower damage/increased ability costs and cooldowns
-Allows for nontraditional character designs such as a lightly armored "glass cannon" melee character that does large amounts of damage if not countered properly, or a plate armored caster tank with cooldown penalties.
Ranged vs. Melee:
-Again, should be handled per-class rather than class archetype
-Allows for melee/ranged hybrids and melee casters
-Melee should do more damage than ranged with everything else equal.
-Example: a plate-armored caster tank with melee abilities. Does as much damage as a normal caster character, except that it would trade ranged damage for heavier armor.
This way, every character stays relevant at all times. There would be a large difference between warriors and casters, but neither of them can scale too quickly. This would also encourage use of a balanced team build instead of making a team out of casters and rushing to level/gear.
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6) No health bar/dying and losing all upgrades for any mistake is annoying. No further explanation needed.
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7) Hardcoded/non-remappable controls. No further explanation needed.
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8) First-person games where movement is hardcoded to Up=Forward/Down=Back/Right=Turn Right/Left=Turn Left - with no sidestep buttons.
Elder Scrolls:Arena controls are a prime example of that problem. Arrow keys to move and turn, no strafing, J to jump (???), hold & move mouse to attack. What was Bethesda thinking back then?
So that means that while moving, my right hand must be on the arrow keys so my left hand can operate the letter key controls, but that locks out the attack command except if I want to put the mouse on the floor and move it with my foot.
In combat, I can put my left hand on the arrow keys and use my right hand for the mouse, but now I can't sprint, jump, or use the cast menu except if I want to use my nose to push those buttons.
Even Might and Magic 6-8 had similar problems - MM6 had hardcoded controls and in MM6-8, strafing was too slow to be useful.