It can't be the AC system. "positive/additive" AC is just plain superior to thac0, end of story.
The designers of 2e wanted to change it, but TSR wouldn't let them because they wanted it to be compatible with 1e modules. Thac0 was invented for that reason.
It can't be the skill resolution system because let's face it, 5e is simpler and better.
I don't agree. The skill resolution system in 2e is also very easy to use. There are no DCs to remember either. You simply roll under your stat and apply a modifier. In addition, 2e skills are far more granular, which allows for a more rich and varied experience. IMO, 5e went overboard by lumping everything under large umbrella skills. It makes no sense for example that anyone with Athletics can swim, let alone do it in armor.
It can't be the magical items, because 5e brings the old school back and the atunement rule is superior - but if you don't like it very easy to remove.
Atunement first appeared in 2e (see Ring of Sustenance). Many people I know hate atunement in 5e, and they don't play with it. I certainly don't need a rule to limit a characters use of magical items. With that said, many of 5e's magical items are just useless when compared to their 2e counterparts.. Take a look at how the scimitar of speed in 5e functions.
It can't be the ability scores because 5e is much more regular and "fairer" - a 13 is worth something now.
Every odd number ability score is NOT worth anything and hasn't been since 3e. Sure, some of the 2e charts can be improved on, but at least the ability score didn't just represent a single modifier. Ability scores since 3e are pointless, they might as well just be a single modifier.
So what is it? Is it the multi-classing?
In someways 2e multi-classing has its advantages. You can actually create a fighter/cleric or fighter/thief/mage at first level. you can realize your character concept from day one.
I think BA went too far in 5e. Sure, D&D has suffered from modifier porn since 3e, but now it still sufferers from hit point bloat. I'd rather have a system like 2e in that regard. In fact, 2e was wise to put a cap on AC at -10
The absence of warlocks, barbarians etc?
Those are kits in 2e.
I personally don't care about saving throws, but I don't mind a chart either. With a chart the system can be less linear.
Yes, less hit points a good thing in 2e.
A good system has many different initiative system options. 2e had several to pick from. Of course, I do miss weapon and casting times.
Spell disruption is great, but I didn't care for 3e's concentration check rules.