Miss all, what was already mentioned in all posts above.
It's hard to explain, but IMHO old PE was made with love from those, who create it.
Now it looks, like it made by someone, who don't care at all about what he doing.
Miss old natural shape of continents, when it looked like real life ones, not like now - "Quadratisch. Praktisch. Gut." (c) ("Square. Practical. Good.")
Miss attention to details.
Miss old cute places and all of them was unique, you could look at any screenshot even with only ground/sky and recognize that place.
Miss old unique ouposts, towns, Minopolis, Hadesheim, strange structures around included, broken vehicles, Umbranoids villages etc.
Miss Billton Towers, where I had and still have apartment, with good ocean/trees view (now all I see - huge "cow").
Miss my old furniture/decorations that broken for 3.5+ years.
Miss my old clothes, that broken for 5+ years (and even more broken now).
Miss old cute Molisks, Argonauts and normal small height Faucervixs, Umbranoids etc.
Miss old mining (including underwater one), where you need to put probe/bomb, detonate it, print claim and when you got globe only when last pile excavated.
Miss old beacon system, when you could loose it any time, before you pressed that red button!
Miss mobs without crazy regen, HP and speed.
Miss my old speed of running.
Miss that feeling, what during each hunt, you could loot something special, not just oil, oil, oil.
Miss PED's and items in loot.
Miss whole old Calypso and PE feeling, what I would like to get - 1x1 copy of old Calypso but enhanced with new engine.
But we will never get all that for sure, all what left our memories and screenshots, it was good old times, I miss them