Worse weapon loadout system. Two primaries make every fight a tedious chore with enemies who have too much life and drop too little ammo to give your heavy slot enough use to make up for the lack of shotguns, fusions and snipers. Those weapons being in the heavy slot was a bad design decision for PvE in order to balance PvP. At end game rockets are still the king of PvE content (utility wise) which makes using shotguns and snipers useless.
Supers, grenades, and abilities are also now much less frequent which added another way to really approach the game. Now you have far fewer ways to vary encounters by playing around with your weapons and abilities because everything has been neutered and streamlined for the sake of balance (PvP balance mind you). This also adds to fights feeling more drawn out.
Additionally, enemies now scale to your level which compounds the above problems. Why am I 305 playing a 240 nightfall and losing my shields in 3 shots even when no burn is active, but in the raid (level 270) I can take about 15 shots before my shields even get into red? You never feel like your power level has gotten you anywhere because enemies now scale with you.
I also don't think the strikes or nightfalls have been an improvement here either. Those were my favorite non raid activities in D1 and now I refuse to touch strikes because theyre long, boring, and I'm still fighting large bullet sponge bosses, and now I'm not even getting loot to make it worth it. Nightfalls having permanent time limits was another bad call imo, especially so because the mechanics for increasing time are typically the "shoot anomalies" modifier. This essentially means play hide and seek with little bright lights in order to buy your team enough time to complete the NF, and unless you watched a video on where they are, youre likely running the nightfall more than once by necessity since odds are you aren't finding them fast enough the first time through to buy enough time that matters. I want to shoot enemies and play the mission, not have a scavenger hunt in obscure areas in order to keep playing the mission (where failure means starting over).
The raid is also a big step down from those in D1 which is the biggest disappointment to me. Raids are why I play. Leviathan is not rewarding from a loot perspective nor a "fun" perspective, with the majority of the rooms and encounters being retreads of previous mechanics.
The story is better from Vanilla destiny but not a step above what we got in TTK (probably on par) and even then its pretty lackluster when compared to most non destiny stories as well.
Infusion system is worse now that weapon types are specific prerequisites for infusing and the mod system hasn't been anywhere near the changes most of us would have hoped for based on how Bungie talked about them adding variety to gear. Weapons and gear are now super generic and lack any meaningful unique abilities like those in D1, and the new additions of grenade launchers (lol) and SMGs are completely trivial.
I could keep going but those are my major issues with the PvE, and I can't for the life of me believe people thinking QoL improvements like not going back to orbit are worth the major step backs in terms of gameplay.