The mecha are designed in a way that if part of Troperion Omega is destroyed, that part can detatch without causing more damage to the rest of the systems.
Aldous is an Ace Pilot, Bernard is a master marksman and fencer, and Charlie is intimately familiar with Omega's systems. The combination lets them each focus on their best talents without dividing their attention between tasks.
The combined mecha is designed as such so there are multiple redundant pilots, ensuring that there is always someone to control the mecha.
Subverted: Alpha, Beta, and Gamma have obvious linkage systems, but they're redundancies from a scrapped project.
Double Subverted: When they're in a pinch, the chief engineer digs up some code that allows them to combine.
Breadbot, Pepperonibot, Tomatobot, and Cheesebot combine to form the invincible Extra-Large Pizza Delivery!!
Several drunken teenage drivers get into a horrible four-way car crash. However against all odd this causes all of their cars to fuse together into an awesome giant robot. They are elated and take their new giant robot for a drive and get into another accident.
Instead of something cool-looking and badass, the combined form is just the individual mecha welded together into what vaguely looks like a new one.
Zig Zagged: Alpha, Beta, and Gamma are not designed to combine. However, with a blowtorch and the power of GAR, the engineers figure out a way for them to combine...but it wasn't designed to do so, and stalls.
The combined form either requires all three pilots to work in unison, which is awkward at best, or reduces two of the pilots to passengers while the third controls the whole thing, something apt to create resentment.
Bernard and Charlie convince Aldous that his mecha is an essential part of the whole and he returns with a vengeance.
The advantages of the combined form outweigh the disadvantages, particularly when the individual mechs have bought time to combine.
The combinedd form allows there minds to "meld" together for a short time, making them even better in combat.
Each pilot is in charge of a different aspect of running the mecha, combat, weapons systems, navigation, and other specialized operations that no one person could manage on their own.
The combined form is very unusual and difficult to control, and arguments break out between the team on how to use it.
The Combining Mecha is made of Mechanical Lifeforms. The fusion of their bodies forms an awe-inspiring titan, but the fusion of their minds forms a deeply troubled individual with the mother of all identity crises who just so happens to be very, very large. And if they separate... Will they be the same as they were before they combined? And what happens to the combined form's identity when its components separate? Is it sleeping, comatose, or dead?