If you do not include equipment like weapons or armor, then you need to include something as a "stand in" for those things. Otherwise, like FFX-2, the only interesting thing about its battle system was the ability to change jobs as the stats didn't really matter at all (because stats were permanently set by level and there was no way to guide growth, so no real customization beyond figuring out who had the best stats for which jobs and making sure that's all they had equipped).
Most players want to be able to customize their characters in some way and make them feel "unique". Weapons and Armors are an easy way to do it. It allows you to customize stats, resistances, attack types, special bonuses (like health regen or counter attack), and other things.
So, you're going to need to invent some kind of system to take the place of Weapons and Armor so that players still feel like they can make important decisions about their characters. Final Fantasy X-2 does not do this. Sure, they let you determine the buy order of most of your skills... But, you're going to get all of those anyway. There's not really any way to "break the mold" in terms of the game and feel clever about doing so. It's like the Crysterium from Final Fantasy 13. Sure, it looks like you're customizing your character, but you're not. What you're doing is moving only along the lines the game devs wanted you t move along and giving you only the stats they want you to have.
See, most battle systems in RPGs run as two types: "grindtastic" or "gimmicky" systems. Grindtastic systems are systems that allow for very little customization (many of these even include lots of weapons and armors to use!). So, you will find the way the devs wanted you to play the game and only ever play it like that. You'll essentially be mashing "Attack" 90% of the time. That's not a good battle system. "Gimmicky" systems are systems that have a lot of random number crunching or weird features that make the player feel like there's a lot of work put into the system... even if the system is still fairly repetitive.
So, what you essentially need is a way to make players feel like they can completely customize how they want to play... while also removing weapons and armor. It can be done, fairly easily in fact. It's just... doing it well that might be the challenge. So, what if you adopt a system that uses "Passives"? As in, you gain a level, you maybe obtain two passives that you could only equip one of. Or, maybe you could obtain 3 passives and you can only use 1 at a time. What if your passives fell into categories? Offense, Defense, Movement, Special, and Skills? What if as you leveled up, you could equip more Passives under those headers? Maybe an Offense Passive would be to grant a 30% critical hit rate bonus. Maybe a Defense Passive could be to have a character automatically "cover" another character with low HP and take hits for them? What if a Movement Passive was something that gave you a chance at an extra turn after you used attack? What if a Special Passive could allow you to absorb lightning damage and turn it into MP? What if your Skills Passive was just the type of Skills you could equip on a character (Magic, Sword Skills, Necromancy, Thievery, etcetera)?
You could easily eliminate Weapons and Armors, but you'll need to replace them in terms of what they were meant to do (they're meant to add diversity to combat and to give the player a level of control over their characters).
Open up some options and think hard about how to give the players things to do with their characters since they cannot choose what equipment they can use.
