I disagree that RuneScape's skilling system, in practice, was ever good.
Each skill is essentially standalone. A better woodcutting level only helps you when woodcutting. A better firemaking level only helps you when firemaking. Same for smithing and all the others. Leveling these skills simply unlocks further content to train these skills. Any exceptions are simply band-aids to the original design.
All skills are overwhelmingly solo activities. Sometimes having more players training can impact the others, more so back in the day than now. The best iron mining spots, which provided the best mining experience of course, could only hold one player. The best hunter spots would highly competitive (chinchompas, salamanders). Then you have totally instanced skills, like farming and all the artisan skills. Dungeoneering was the exception, but now sinkholes, buffed solo experience, and daily challenges make that moot. Essentially, RuneScape was a solo RPG with multiplayer chatting unless you went into the wilderness...
Many were useless (and some still are). Firemaking is pointless. The artisan skills are mostly useless because infinitely better gear is obtainable from PvM. Divination is essentially useless because Invention was delayed for so long (and it's sad that Invention is required to make the skill useful; why bother making it in the first place?). Gathering skills are obsolete because killing your typical slayer monster, let alone the big meany spiders, ghosts, enlightened rocks, and incompetent pet owners followed by giant worms-snake-dragon-spirits are better means of obtaining most resources than mining/woodcutting/harvesting/whatever them yourself.
Resources/training is tiered or imbalanced. Why was mining iron better than mining rune? Why were willows better than yews? Nowadays, gathering skills are mostly useless; you can get more adamant ore ore during an hour of high level PvM than you could in hours of mining it. Even worse, you got less adamant bars mining the ore and coal and then smelting it than when when killing Aviansies with crappy gear all the way back in '07!
So many skills were designed without any future planning. Rune two-handed swords being level 99 Smithing showed immense lack of foresight. More so when you consider rune equipment being level 40 equipment later (and worse, at the time, weapons didn't have requirements!). Soon enough comes dragon equipment, level 60. And how do you reforge a dragon square shield? Oh, that's right, with level 60 smithing. Only 33 more levels and you can make a greatly inferior rune square shield! Even skills released recently have terrible content at the top. Summoning only has a handful of good familiars with little balance. The best combat familiar primarily uses range and requires 99 summoning, no magic/melee familiar even compares; the Pack Yak is the best, by far, beast of burden, greatly surpassing the War Tortoise simply due to its banking ability, let alone the +12 slots; the Unicorn stallion was the best healing familiar for non-bossing activities prior Evolution of Combat; and... all the others are useless. Even Dungeoneering was useless beyond getting the necessary Chaotic weapons, which only required 94 to get all the useful ones of the time (rapier, crossbow, staff, and maul), and yet the skill went up to 120...
Only nostalgia can hide the fact that RuneScape's skills were poorly implemented from the start. AFK and devalued accomplishment aren't the problem. Terrible design and planning are.