I'll break it down simply.
First, let's examine what a roleplaying game actually is.
A roleplaying game, by its basic, general, non-exclusive definition, is a game that is designed to draw the player into the role of the character.
The JRPG approach, in general terms, uses the storytelling technique of escapism, specifically player-into-character, by providing a linear, predetermined storyline for the player to follow and escape into the role of the character. Escapism is something that can be proven to be effective; examples include somebody crying during a particularly sad scene, or coming to hate the villain of the story, or wanting to see the hero win etc. It doesn't necessarily work in all cases; there are certain people who are completely disconnected from the story in that sense. However, this is something that definitely can work, and statistically speaking is something that can be said to work more often than not, and as such it is a valid approach to the objective that the genre is intended to meet.
The WRPG approach, in general terms, uses gameplay mechanics that are intended to create the illusion that the player is in complete control of the character, and that by extension that he is the character, by creating a non linear storyline with choices at his disposal that can result in a number of different storyline outcomes. However, this approach is not something that can be proven to be effective, and basic logic would dictate that it isn't.
Dialogue options generally number in the single digits at most, are not necessarily reflective of the player's personality, and yield into no more than a few potential variable outcomes. The choices at your disposal do not originate from you, the player, but are simply presented to you by the game itself. The total number of available choices that the game presents before you in proportion to the total number of available choices there would realistically be in any given situation is astronomically small. As such, basic logic would dictate that you would have to be of an inhumanly passive nature to feel in control of your character given just how limited the choices before you are, rather than largely restricted and separated from the character. Statistically speaking, humans are not of such a passive nature, and generally will make an innumerable amount of choices that aren't dictated by straightforward rules or routines dictated by others. So while this approach could be effective in some extremely rare, quite frankly odd cases, statistically speaking, it would be extremely ineffective in far more cases than it wouldn't, and I would imagine in the cases of everybody who posts in this forum. So ultimately, the approach quite simply can't be proven to be effective, and logically speaking, it generally wouldn't be.
So while a non linear game can't necessarily be said to be a bad thing, it can be said to be, in all likelihood, a bad roleplaying mechanic, and by extension, a roleplaying game that defines itself by this approach (pretty much every Bethesda game, the Fable games, the KotOR games etc.) can in all likelihood be said to be a bad RPG.
A side effect, as well, is that the creativity of the developers is filtered through multiple different branching storylines, and as such the quality of any single given chosen storyline is not being maximised to the full potential of the developers.
Another quite common side effect is that often, NPC dialogue is designed in a way that it can respond to a number of different dialogue options. This can be especially seen in a lot of Bioware games. The effect that this creates is that the dialogue, in a lot of cases, doesn't feel like it flows naturally.
A number of other side effects can occur due to this approach. The KotOR games, for instance, had a large emphasis on how your choices dictated your alignment, with the whole light side/dark side system. However, rather than putting some real thought into how they would implement this into your choices, the vast majority of these dialogue options corresponded with generic evil/good/neutral mindsets, but beyond that came across as really forced and unrealistic, to the point where these choices weren't so much based around the player's own personality, but around what response he wanted to see the most, or what path he wanted to take.
Really, it's a terrible approach to the genre.