The greatest problem is that plot elements which are introduced in a unified story section of the game are often developed or resolved in certain missions on one plot path during a split story section. For example, a major villain named Archibald Grims first challenges the heroes in the first few missions of the game, and recurs constantly through several battles. However, Archibald often only reappears to fight the heroes again on only one of the paths during split path sections. Furthermore, Archibald is finally defeated by the heroes for good during a split path. As a result, a player who takes the opposite paths that Archibald Grims doesn't appear on will be introduced to Grims, then wonder where he went and never get to see the resolution of his story.
This gets even more complicated when plot elements and characters are introduced during one of the branching sections. For example certain villains, such as one of the Inspectors, first appear on the battlefield during some early branching sections, but then reappear during a unified section. If a player picked a different path, then the player is suddenly introduced to a character who the characters in the game have already met. And following the problem listed above, these characters can also have their stories resolved during split story sections.
My brother actually experienced the result of this. During his first play through of the game, the Machinery Children were introduced off-screen, on the plot path my brother passed up. Later, they showed up to fight the main characters during a unified plot section. After that, the Machinery Children were defeated for good on a story branch my brother did not see. As a result, the Machinery Children were introduced off-screen, made a brief on-screen appearance, before they died off-screen.
The story becomes even more convoluted as a result of how the characters are divided up during split path sections. First off, there are two rough plot paths that the player chooses between during each split, based on the teams who go on the different missions: the Super Robot path (which always includes Kyosuke Nanbu, the main character) and the Real Robot path (which always includes the SRX team). However, the characters who make up these teams, and thus the sub-plots the teams deal with, are not consistent.
For example, a major sub-plot of the game is the rivalry between Sanger Sonvolt and Wodan Ymir. Wodan Ymir first appears on the Super robot route during the first split, and the first time you get to fight him (and where Sanger first show up) is again on the Super Robot route during the second split path section of the game. Then Sanger and Wodan both play a prominent role during the third unified section of the game. However, Sanger and Wodan finish their decisive battle during the third split path section on the Real Robot route.
Because of complications like this, the player is 100% guaranteed to run across the weird plot problems I outlined above. The player will never be able to see more than a few plot threads go from introduction, through development, to final resolution in one go through the game. And since the player can alternate between following the two different general routes, it is possible for the player to miss out on parts of every plot thread in the game.
This system has a lot of room for improvement. A good model to follow might be Final Fantasy VI's split scenario system, where the player had to go through all three paths during the one time the game split into multiple paths. A similar example is in Suikoden 3, where the entire first half of the game consists of split paths, where the player has to follow all of the routes to completion in order to reach the second half. If the Super Robot series let the player see both paths, then playing through OG2 would be a lot less confusing.