How about just removing shops? If a player needs certain items, how about adding some zones or some quests that can provide these items? For example, add a quest that rewards the player one inscription or rune of his choice (perhaps a different quest for inscription and rune).
Shops could still spawn in certain random locations. That way when you find a town would be an actual surprise and possibly a nice boon. For example, there is a chance that a small elvish town with a shop will spawn in the old forest or a few other locations. Depending on where the shops spawns, you will get certain items that you can buy.
About the inscription problem: how about making these always the same:
* Regeneration: Heal 50% max hp +20hp over 5 turns (70 at 100hp, 530 at 1000 hp)
* Heal: Heal 40% + 20 (60 at 100 hp, 420 at 1000 max hp)
* Movement infusion: always ~800% for 1 turn
* Shielding: 30% + 20 (~380 at 1200 max hp)
This way they scale with hitpoints. This allows players to maintain the usefullness of their inscription choice, wile also adding usefullness to HP increasing thins like CON.
The player can still find insripctions and runes, keep a healing / movement / whatever infusion in his inventory, and choose what to use. Allowing these inscriptions and runes to scale automically as you level removes unneeded complexity from the game. The real choice should be which infusion or rune to use, not how powerfull the one is that you find. Giving all players acces to the same healing skills that scale on hitpoints will possibly also make the game easier to balance.
Note: Inscriptions are arguably something in-between talents and items. They are not really talents, since you can 'equip' them, and they are not really items, since they work like talents. For equipment, scaling makes sense (you find better weapons as the game progresses). For talents, scaling works differently (talent often scale off equipment and other stats). Since runes and infusions are somewhere between items and talents, there could be a bit of item scaling (akin to weapons) while still preserving stat scaling (akin to talents). For example, a healing rune could variate between healing 30-50% of your max hp. I think players might even start with the highest possible bonus, possibly giving them a small penalty for changing their runes since max runes would be rare to find. Just some ideas.
By the same logic, movement infusions could scale on dex. For example, dex is generally somewhere between 10-80. This difference is to big, so we make it smaller so it is only about 20% difference:
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(dex + 250)*2 = percentage movement speed increase (somewhere roughly between ~520 and ~700%)