Loss of community, my first MMO only had around 250 regular players, the game wasn't driven by the development team but instead the interactions of players. You quickly knew who the PKers were (yes open world PvP where when you died you actually could drop your items, including your weapon which may have taken you 3-6 months to save for), you knew the figure heads for the major factions, you knew the best merchants and crafters. It just had a great sense of community as you pretty much knew who everyone was.
This was the typical experience I had in MMOs from 1999 onwards until World of Warcraft came along, suddenly we had thousands upon thousands of people playing on the game all active at once, but for me this destroyed that sense of community, I usually end up leaving games this day and age as its often a see someone once and never again scenario.
Level caps!! Oh dear god why was this introduced? Asian MMOs had the way forward here by having no imposed level caps, you could just level and level and level some more if you could withstand the grind. Ok the levels eventually turned into to get from one to the next would take 6, 12 or even 18 months of playing but it was nice to know their was no level cap. Now its all level restricted zones taking away from the ability to just go on an adventure.
Instances, while from a story perspective they are great. I really miss the days of fighting through a dungeon (some took 3-4 hours to make it to the boss) to find another guild had also fought its way there as well. Battle would ensue (open PvP) and you would slog it out with the other guild managing your potions etc knowing that if you used too many in PvP you wouldn't have enough to kill the boss.
"Modern guild systems" the first few MMOs I played offered the same guild controlled keeps etc as we have today however they have in my opinion taken massive steps backwards as well! I remember when you practically had a fully functional guild website in the game, no alt + tabbing. They offered a notice board, a place guild masters could post guild rules, when they were organising events, what items the guild store contained and if any were out on loan. It was all available in one place! Also you had the option of as many different titles in the guild as you saw fit, no three or four tiers where you couldn't change the rank name! Hell if you wanted to be called "Kitty Lover" as your guild rank you could!
Its not all bad though, isometric 2D graphics have been replaced by glorious 3D worlds. Stories and scripts have become common place giving you more to do than just a pointless grind. Difficulty of content has vastly improved requiring actual thinking rather than the bashing of the same skills over and over for a boss that has very little AI.