The bounce arc is too high to make use of on certain stages so I think that needs to be taken into consideration too.
I feel as though this is the most important thing to note.
Bouncing Gordos lose a lot of potency on certain stages with platforms, slopes, stage hazards, and on stages that tilt. Using EVO's stagelist as an example, here's what type of Gordo I would use depending on the stage.
Bouncing Gordo: Final Destination, Smashville, Town & City, Battlefield
Standard > Bouncing (probably): Halberd, Castle Siege, Delfino Plaza
Standard Gordo: Final Destination, Smashville, Town & City, Battlefield, Halberd, Castle Siege, Delfino Plaza, Lylat Cruise, Duck Hunt
As you can see, I feel as though Standard Gordo is much more useful on most stages. And here's some reasons why I feel as though you should avoid Bouncing Gordo in the other stages.
Halberd: While on the floating portion of the stage, the large platform perfectly shields any opponent that's under it, due to it's size and because there are slopes below it. While fighting on the Halberd itself though, this no longer becomes an issue.
Castle Siege: While lopsided, Bouncing Gordo can be effectively used on the first transition of the stage. However, things get dicey on the later two parts of the stage. The second transition because statues kill Gordos (though this also applies to default Gordos), and the third transition because of how the stage tilts. In particular, the third transition is the main problem, because the ground can completely erase a Bouncing Gordo sometimes when the stage is tilting. Overall Standard Gordo would be better here for consistency.
Delfino Plaza: Tons of platforms and slopes to take into consideration here, which can lead to many unfavorable Gordo Bounces. It can be mastered with perfect understanding of the stage, but you probably would want to consider using Standard Gordo more for this stage instead, since the results would be a lot more consistent.
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Lylat Cruise: Don't even bother picking Bouncing Gordo here. Even if you take into account the three platforms which opponents can hide under and the far slopes of the stage, none of this matters because the stage tilts. It literally eats most Bouncing Gordos that you throw before they even get a chance to bounce once.
Duck Hunt: Quite simply, the ducks can ruin your Bouncing Gordo shenanigans outright. Don't pick it here.
Overall, even if you don't take specific matchups into consideration, Bouncing Gordos are hindered by the stages that are picked. While Standard Gordos are far less susceptible to this. Therefore, your best bet is usually just sticking to using the Standard Gordos for most situations.
This is coming from someone who also likes to use the 3122 and 3322 sets. I hope this helps.