about your first point it is supposd to be hard so you need to plan i was able to get all stats up to 40+ tamed all girls in the dungeun and ask them for there genex got to level 10 and got all the genex except lynx and wispers becouse it was not compateble whit the true hero run as for thr dungeon it is not meant to be finishd some rooms dont have a use in the first chapter the lower rooms but i was stil able to get evrthing ecpet some level 2 trianing rooms and nothing on the level 3 trianing rooms and still got money to spare
you are richt whit your second piont and your third point is based on prefernce, i personale think he did a creat job ate story progresion
as for your fourth piont mabye he will develop your chapther 2 suit based on the route you are on something like superman for hero batmen vigelantie and antihero deadshot like