[RPG] PC created magic items and how to scale charges

You do not generally use wands or wondrous items for offense. The artificer class from Eberron Campaign Setting can make it work, but for pretty much everyone else it just costs too much no matter how you do it. Wands and wondrous items that use spells are usually used for utility, stuff you can do out of combat.

The reason why is because in combat, the most precious things in the game are actions. The vast majority of combats are decided in the first 2-3 rounds—many in the very first. You only have so many opportunities to do something to change the outcome of the fight. That means that your actions in combat have to be very, very potent. Spells can often do that—but they need to be reliable. That means high saving throw DCs, that means high caster levels, and so on, and magic items do not offer these.

In contrast, out of combat, you can take more time. If something only has caster level 1st and so only lasts one round: no problem, you can take the time to just keep using it. If something has a save DC of 11 because that’s the minimum for a 1st-level spell and magic items use the minimum possible value, that’s fine because it’s not an attack, it’s healing an ally or lighting a hallway or whatever.

So basically, your concern is rather moot: the real answer is that neither of these things is used for the purposes you’re imagining.

This does lead us to the more direct answer to your question: 50 charges is more-than-enough for a whole lot of spells. If you find a wand of magic missile with caster level 1st, you simply don’t care that it’s only got 50 charges: you are going to reach a point where caster level 1st magic missile is just not worth using at all because your actions are too precious. Might as well see the savings up front. After all, command-word items cost more than double what a wand does. That’s a really big deal.

TL;DR: Command word items cost double what the comparable wand does, and for most spells, 50 charges is more than enough as it is. Many spells just aren’t useful when cast from items, and that includes almost all you would attempt to use offensively.

Dungeon Master's Guide, p. 141 (emphasis mine)

Spells

Some magic items allow the user to cast a spell from the item. The spell is cast at the lowest possible spell level, [...]

The lowest possible spell level to cast a spell is the default level of that spell. Cone of Cold is a 5th level spell, thus it is cast at 5th level. Ray of Enfeeblement is a 2nd level spell, thus cast at 2nd level.