Dark souls II suffered from several things, not necessarily from one reason or factor at once.

Expectations

After Dark Souls I came out players expected improvements on too many fronts they loved. When the game was not designed that way, some felt betrayed in a bad way and that earned the game a bad reputation.

Storyline Flaws

In DSI the quest for the Lord Souls logically stemmed from a single door being locked by the Lordvessel contraption and this made sense, but in DSII the Shrine of Winter is the only passage way around a pile of rubble. Hardly an obstacle worthy of an undead, nor reasonable for the storyline, even if it could now be circumvented by collecting millions of souls instead of the four great ones.

Enemy Design and Placement

In DSI enemies were part of each stage, both for the better and the worse. DSII reversed this aspect but took this focus too far at some points. In DSI the stage was designed to both challenge and betray the player so that once the trick was figured out the magic was gone. In DSII the enemies were the focus so that they would quickly readjust after having their advantage taken from them, however early stage enemies relied too much on exposing each other to danger purely in order to leave the undead open for that one nasty retaliation that would seal his fate. The result of this was that enemy fights became very tedious because the battles were focused on stalling moreso than actual engagement.

For DSI ranged-and-infantry ambushes function in a very traditional manner in which the player would have to carefully pick which one to neutralize first before progression could be made. In DSII the same obstacle is often represented by placing several infantry in a single room while the player is being pressured from all sides only to find out that the whole group could have been circumvented in the first place. Sadly the game did not offer means of reversal so that once the player is occupied with too many enemies he or she has to wittle down one at a time all while exhaustingly avoiding damage. In a sense DSII ended up forcing the player into a downward spiral of escalation by continuing a worsening chokehold with stalling tactics without enough means to break free.

The Iron Keep can be a major hurdle for players in concerns to how well the player can progress to the Smelter Demon. Alonne Knights are very fast opponents compared to most players, whom likely play the area for only the second major boss and limited experience with swift movements and ranged barrages. Even in very limited numbers Alonne Knights can put a player under heavy pressure. Sure the Smelter Demon is optional but it is understandable how it becomes a less appreciatable opponent in an area that already leaves most players battered before the passively life draining battle even begins. With little information on the area layout it is possible for players to get stuck here for far longer than what would provide enough merit to contribute to player experience.

Larger Areas

In DSII areas are larger to allow more movement for the player to find new approaches but since the game left so little options to make this accomplishment worthwhile it is widely regarded as empty space. The player can run out of stamina several times to move from bonfire to bonfire without leaving from one room or area to another adequately or without having made a significant difference for the combat the areas were designed for in the first place. In DSI areas were compact and interconnected and filled with mechanism, secrets and oriention from area to area in order for the player to prepare but DSII repeatedly leaves little if any of these options in the game.

PvP

DSII focuses heavily on online gameplay experience and most combat in pvp works fine and balanced without causing disturbances. Katanas and curved swords are inconveniencing to face if not the least, mostly because of the netcode and poor adjustment to practical gameplay mechanics but for most other weapons and equipment this is hardly the case.

Stat scaling was a much greater hurdle in DSI than in DSII because in DSII stat requirements are lower and player can find their most suitable weapon types mostly early in the game and the same goes for armors. Soul Memory is its own problem because the Agape Ring can be out of reach. A beginning and inexperienced player would have to die several times before even obtaining the ring only to find out that by that time it had grown increasingly pointless with every failed attempt. Hacking is also a problem in repeatedly victimizing the offenders less easily than the average player.

Covenants

In DSII covenants focusing on pvp victories and invasions are difficult to finish because players have to face both soul memory, other players and connection if not all at once. The more tedious it gets the easier the justification is made to rely on unbalanced weaponry or perhaps even illegal programs, be it macros, modifications on the side of the offender or worse, those of another player.

Soul Memory and Soul Vessels

The option to reallocate points to character stats is conventient but can cost a player more souls than would benefit them in order to create a suitable build. Soul memory may be a repeated problem but it can be a tormenting and haunting shackle to players whom have to yet find out what suits them most. Most players would reroll and grind the Giant Lord with the Agape convenience to avoid having to face several optimized characters and their builds without an oppertunity to learn the basics of pvp.