I played through the full game with a Druid last night.. Using your template here's my suggestion.
Save/Load
No problems here.
Waypoint System
Well done.
Normal, Magic, Set, Unique Items
Needs much more diversity. The Normal items arent even comparable to the Magics, and if you've played D2, no such magics exist. There was like 5 magics in total.. Sets + Uniques I can't even comment on because even after Andariel, not one dropped. The map was 95% cleared, ( Skipped the ridiculously overpowered cows ) Maybe put in Rares?
Trade System
I played on local, no point trading with my brother across the hall eh?
Stash System
Decent. The placement of the stashes ( On top of eachother ) makes it easy to misclick and give your precious item to someone else.
Custom Abilities
I agree with skullbasher here, the spells were very basic and organized the wrong way. My Druid for example.. ( Even though you said he was horrible )
Armageddon: Lvl30 Elite in D2, Very weak and obtained at low level in ATOC.
Werwolf: Skill obtained early on in D2 ( lvl6 I think ), made into a lvl18 elite in ATOC.
The skills in the spellbook were also kind of retarded.. My siphon did 10000/sec for 60 seconds, and brothers strafe did 5000 an arrow with 10sec stun each? We both used at the same time and Andariel was owned 3 seconds flat.
I dont mean to be harsh but some skills need to be revised.. Werewolf and Javazon skills are insanely overpowered if you don't take into account how hard the enemies are. Skull was also right to point out that there are three skill trees per char. If you plan to extensively improve the RPG, add a second selection choice after choosing the char type.
Example: I choose Sorceress.. I then have a choice of either being a Fire/Cold/Lightning Sorceress.
That was each char wont have a jumble of skills from each tree.
Gambling System
Tried it a few times, wasn't worth the gold.
An extended inventory system
Doesn't work the way I think you intended it.. If I have all my damage items on Inventory 1, and switch to Inventory 2 to pick up something, my damage goes away. I died a few times thinking I was ready but ended up doing 100 dmg a hit instead of 900.
( 500 --> 5000 with Werewolf crit )
Quests
All the usual ones I saw in Act1, the rewards were hardly worth it though. ( Den is +1 Skill ? Maybe level up 1? )
Cows
Were you on drugs when you made these?
A PK Areana
No point testing it, Javazon was Chaos dmg and fortified armor. Werewolf was same as druid. I'm sure its okay.
Mercenaries
I tried one out, they were okay but they could use a skill makover as well. Only leveled her to 6 before she was just a useless XP leech.
Original NPCs
Dont accurately from what I could tell.
Cinematics
Just an intro. You should add some Boss cinematics
Set Item Completion System
Didn't get a chance to use, never found a set!
Take from my rant what you will.