There are several reasons. Most of them are probably a matter of taste though.
The quality of writing varies greatly from NPC to NPC (imo). While I found Neera's content in BG2 quite enjoyable, I couldn't bear having Hexxat in my party. Some of the encounters and quests are also much more challenging compared to quests attached to the old NPCs. The most annoying issue for me (and the main reason to create this mod) was the way how almost every new NPC tried to force themselves into my party. That's why I have added a "passive" NPC component to this mod. The current version of the games also contain a number of (quite serious) bugs, but that issue should be solved with the next patch.
It is mostly a matter of taste, i.e. the new NPCs appear more than NPCs from a mod than vanilla BG1 NPCs.
I agree that their quality is quite different from each other (again subjective judgement), from interesting Neera to Baelot at the level of a one-day-NPC. They come with quests and romance options like a mod NPC. They are still bugged even in the latest edition.
In a modded game, e.g. in EET they fit in, (when you have BG1NPC romances and other mod NPCs alongside with them) - in a vanilla BG1 game they may appear odd.
In this way Argent77*s approach is valid as it makes them selectable - if you play a modded game with other mod NPCs in it, they fit quite well, otherwise you may leave them out at your discretion.
Personally I treat them like any other mod, they are an offer you can take or ignore. (I do not agree that they *force* themselves into the party - it is rather that they make some *grand appearance* that lets you expect more from them than they fulfil.) Compared to many mod-added NPCs they are at a medium-to-poor quality but there are worse...and they can be improved like the original BG vanilla cast was over time...