I can't find anything that predates FF X (2001) regarding universal skill trees, so they may be the first.
I have also not played FF X, but I read there is an active and passive skill set, the closest concept of which is probably dual/multiclassing in AD&D, as for example implemented in Baldur's Gate (1998). This is not a universal skill tree, and has significant limitations:
Non-human races may choose to multi-class at character creation, advancing in two or three unkitted classes simultaneously. Multi-class creatures gain the advantages and abide the limitations of every class, they divide their experience points among their classes, so they progress in levels more slowly than single class creatures.
Humans may not MULTI-class, but can instead DUAL-class, starting from a Level 2 kitted or a unkitted class onward. By doing so, they cease to advance in their current class and start to develop a new, unkitted class from its Level 1. Once they have changed to a second class, they cannot go back to the first. In addition, the abilities of the first class become unavailable until the second class reaches one level beyond the level where the first class stopped. This option may only ever be done once, even if the requirements are met for more than one new class.
And a bit of history: Skills were first introduced by Wizards of the Coast / TSR:
Wizards' version of the game also introduced Skills, which determined how good characters were at the fundamental aspects of adventuring. Previously, these had been largely derived from Ability Scores or simply roleplayed.
BG used the AD&D 2nd edition ruleset (1987):
The 2nd edition of Advanced Dungeons & Dragons attempted to streamline what had become a hodgepodge of rules that only applied in specific cases in 1st edition. As such, it sought to simplify the rules and straighten out contradictions. Character classes were divided into four groups or "metaclasses": Warrior, Wizard, Priest, and Rogue. Each of these groups had a "base" class which only required at least a 9 in the "prime requisite" statistic in Fighter, Mage, Cleric, and Thief; these were intended to be playable in any setting.
The concept of skill trees is rooted in the tech tree:
Before skill trees there were technology trees in strategy board games. These hierarchical graphics represented the number of possible upgrades a player could make to their army to gain a strategic advantage over their opponents.
...which made its first appearance in the original Civilization board game (1980):
Civilization (1980) is credited as the first board game to introduce the concept of a tech tree. The idea of the system popped into acclaimed British game designer Francis Tresham’s head in the late 1970s and it changed the course of tabletop and video gaming.
...which from there on ended up in the 1991 video game edition (and of course numerous RTS games like Dune II (1992)).